<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="/sitemap_generator/default/sitemap.xsl"?>
<!--Generated by the Simple XML Sitemap Drupal module: https://drupal.org/project/simple_sitemap.-->
<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9" xmlns:image="http://www.google.com/schemas/sitemap-image/1.1">
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/</loc>
  <lastmod>2025-11-19T03:43:11+00:00</lastmod>
  <changefreq>daily</changefreq>
  <priority>1.0</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/biophysical-fitness-landscape-design-traps-viral-evolution</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/biophysical-principles-predict-fitness-sars-cov-2-variants</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/biophysical-principles-predict-fitness-sars-cov-2-variants-0</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/few-shot-viral-variant-detection-bayesian-active-learning-and-biophysics</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/epistasis-meets-pleiotropy-shaping-biophysical-protein-subspaces-associated</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/evolution-biophysical-fitness-landscape-rna-virus</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/cotranslational-formation-disulfides-guides-folding-sars-cov-2-receptor-binding-domain</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/cotranslational-protein-folding-through-non-native-structural-intermediates</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/multi-condensate-state-functional-strategy-optimize-cell-signaling-output</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/origin-ionic-strength-dependent-reentrant-behavior-liquid-liquid-phase-separation</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/separation-sticker-spacer-energetics-governs-coalescence-metastable-condensates</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/biophysical-principles-predict-fitness-landscapes-drug-resistance</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/evolutionary-dynamics-viral-escape-under-antibodies-stress-biophysical-model</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/ribosome-associating-chaperone-mediates-gtp-driven-vectorial-folding-nascent-eef1a</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-quality-control-master-modulator-molecular-evolution-bacteria</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/separation-sticker-spacer-energetics-governs-coalescence-metastable-condensates-0</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/multi-condensate-state-functional-strategy-optimize-cell-signaling-output-0</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/entropy-changes-water-networks-promote-protein-denaturation</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/epistasis-and-pleiotropy-shape-biophysical-protein-subspaces-associated-drug-resistance</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/co-translational-formation-disulfides-guides-folding-sars-cov-2-receptor-binding-domain</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/empowering-drug-target-discovery-metabolic-and-structural-analysis</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/systematic-conformation-phenotype-mapping-limited-deep-sequencing-proteins</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/allosteric-communication-between-ligand-binding-domains-modulates-substrate-inhibition</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/systematic-conformation-phenotype-mapping-limited-deep-sequencing-proteins-0</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/native-chemical-chaperone-human-eye-lens</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/switching-active-site-helix-dihydrofolate-reductase-reveals-limits-subdomain-modularity</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/metabolic-response-point-mutations-reveals-principles-modulation-vivo-enzyme-activity</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/accelerating-high-throughput-virtual-screening-through-molecular-pool-based-active</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/avoidance-protein-unfolding-constrains-protein-stability-long-term-evolution</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/effect-protein-structure-evolution-cotranslational-folding</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/dynamic-metastable-long-living-droplets-formed-sticker-spacer-proteins</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/effects-single-mutations-protein-stability-are-gaussian-distributed</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/common-activation-mechanism-class-gpcrs</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/semi-rational-design-and-molecular-dynamics-simulations-study-thermostability</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/adaptation-mutational-inactivation-essential-gene-converges-accessible-suboptimal</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/early-phase-b2m-aggregation-integrative-computational-study-framed-d76n-mutant-and-dn6</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/simulation-guided-enzyme-discovery-new-microbial-source-cellobiose-2-epimerase</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/substrate-inhibition-imposes-fitness-penalty-high-protein-stability</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/chimeric-dihydrofolate-reductases-display-properties-modularity-and-biophysical</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/mutation-rate-variability-driving-force-adaptive-evolution</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/dynamic-disulfide-exchange-crystallin-protein-human-eye-lens-promotes-cataract</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/growth-tradeoffs-produce-complex-microbial-communities-single-limiting-resource</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/accurate-protein-folding-transition-path-statistics-simple-free-energy-landscape</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/proteomevis-web-app-exploration-protein-properties-structure-sequence-evolution-across</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/accessibility-shine-dalgarno-sequence-dictates-n-terminal-codon-bias-e-coli</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/proteomevis-web-app-exploration-protein-properties-structure-sequence-evolution-0</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/trade-offs-between-microbial-growth-phases-lead-frequency-dependent-and-non-transitive</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/absence-selection-quantum-coherence-fenna-matthews-olson-complex-combined-evolutionary</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/evidence-evolutionary-selection-cotranslational-folding</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/optimization-lag-phase-shapes-evolution-bacterial-enzyme</loc>
  <lastmod>2025-05-15T18:56:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/tale-two-tails-importance-unstructured-termini-aggregation-pathway-b2-microglobulin</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/effect-sampling-bace-1-ligands-binding-free-energy-predictions-mm-pbsa-calculations</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/role-evolutionary-selection-dynamics-protein-structure-evolution</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/graphs-topology-and-free-energy-spin-model-graph</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/hybrid-knowledge-based-and-empirical-scoring-function-protein-ligand-interaction</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/transient-protein-protein-interactions-perturb-metabolome-and-cause-gene-dosage</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/bridging-physical-scales-evolutionary-biology-protein-sequence-space-fitness-organisms</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/structure-based-prediction-protein-folding-transition-paths</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/internal-disulfide-locks-misfolded-aggregation-prone-intermediate-cataract-linked</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/simple-model-protein-domain-swapping-crowded-cellular-environments</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-homeostasis-imposes-barrier-functional-integration-horizontally-transferred</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/opengrowth-automated-and-rational-algorithm-finding-new-protein-ligands</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/repurposing-rutin-inhibition-norovirus-replication</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/thermal-stabilization-dihydrofolate-reductase-using-monte-carlo-unfolding-simulations</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/minimalistic-predictor-protein-binding-energy-contribution-solvation-factor-protein</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/catalytic-activity-chaperones-selectable-trait-emergence-heat-shock-response</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/influence-selection-protein-stability-dnds-estimations</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/evolution-specificity-protein-protein-interactions</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/gene-dosage-experiments-enterobacteriaceae-using-arabinose-regulated-promoters</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/merging-molecular-mechanism-and-evolution-theory-and-computation-interface-biophysics</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/simulated-intermediate-state-folding-and-aggregation-provides-insights-dn6-b2</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/influenza-h1n1-pandemic-strain-evolution-divergence-and-potential-antigenic-drift</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/catalysis-protein-folding-chaperones-accelerates-evolutionary-dynamics-adapting-cell</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/contribution-selection-protein-folding-stability-shaping-patterns-polymorphisms-coding</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/assessing-effect-loop-mutations-folding-space-b2-microglobulin-molecular-dynamics</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/structural-and-energetic-determinants-co-translational-folding</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/positively-selected-sites-cetacean-myoglobins-contribute-protein-stability</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/one-shot-germinal-center-model-under-protein-structural-stability-constraints</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/highly-abundant-proteins-favor-more-stable-3d-structures-yeast</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/universal-trend-among-proteomes-indicates-oily-last-common-ancestor</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-quality-control-acts-folding-intermediates-shape-effects-mutations-organismal</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/collapse-unfolded-proteins-mixture-denaturants</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-biophysics-explains-why-highly-abundant-proteins-evolve-slowly</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/robustness-atomistic-go-models-predicting-native-folding-intermediates</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/mutation-induced-extinction-finite-populations-lethal-mutagenesis-and-lethal-isolation</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/identification-conserved-aggregation-prone-intermediate-state-folding-pathways-spc-sh3</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/there-en-route-folding-intermediate-cold-shock-proteins</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/soluble-oligomerization-provides-beneficial-fitness-effect-destabilizing-mutations</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/sequence-correlations-shape-protein-promiscuity</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/thermodynamics-and-kinetics-hairpin-ribozyme-atomistic-foldingunfolding-simulations</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/biophysical-protein-folding-model-accounts-most-mutational-fitness-effects-viruses</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/multi-scale-sequence-correlations-increase-proteome-structural-disorder-and-promiscuity</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/ensemble-folding-kinetics-fbp28-ww-domain-revealed-all-atom-monte-carlo-simulation</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/non-native-interactions-play-effective-role-protein-folding-dynamics</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/de-novo-design-balancing-novelty-and-confined-chemical-space</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/optimality-mutation-and-selection-germinal-centers</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/thermal-adaptation-viruses-and-bacteria</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/interplay-between-pleiotropy-and-secondary-selection-determines-rise-and-fall-mutators</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/stochastic-switching-gene-networks-can-occur-single-molecule-event-or-many-molecular</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/thymic-selection-t-cell-receptors-extreme-value-problem</loc>
  <lastmod>2025-05-15T18:56:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/lethal-mutagenesis-viruses-and-bacteria</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/fog-fragment-optimized-growth-algorithm-de-novo-generation-molecules-occupying-druglike</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/slowly-replicating-lytic-viruses-pseudolysogenic-persistence-and-within-host</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/dna-unzipping-phase-diagram-calculated-replica-theory</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/all-atom-model-stabilization-alpha-helical-structure-peptides-hydrocarbon-staples</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/emergence-species-evolutionary-simulated-annealing</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/identifying-critical-residues-protein-folding-insights-phi-value-and-pfold-analysis</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/sdr-database-predicted-specificity-determining-residues-proteins</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/sensitivity-dependent-model-protein-protein-interaction-networks</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/constraints-imposed-non-functional-protein-protein-interactions-gene-expression-and</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/improvisation-evolution-genes-and-genomes-whose-structure-it-anyway</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/statistically-enhanced-promiscuity-structurally-correlated-patterns</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/universality-and-diversity-folding-mechanics-three-helix-bundle-proteins</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/understanding-protein-evolution-protein-physics-darwinian-selection</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-stability-imposes-limits-organism-complexity-and-speed-molecular-evolution</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/robust-protein-protein-interactions-crowded-cellular-environments</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/native-atomic-burials-supplemented-physically-motivated-hydrogen-bond-constraints</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/first-principles-model-early-evolution-emergence-gene-families-species-and-preferred</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/quantifying-fitness-distributions-and-phenotypic-relationships-recombinant-yeast</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/positive-and-negative-design-stability-and-thermal-adaptation-natural-proteins</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/folding-mechanics-knotted-protein</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/energetics-protein-dna-interactions</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/all-atom-ab-initio-folding-diverse-set-proteins</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-and-dna-sequence-determinants-thermophilic-adaptation</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/statistically-enhanced-self-attraction-random-patterns</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/knowledge-based-move-set-protein-folding</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/structural-similarity-enhances-interaction-propensity-proteins</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/structure-centric-view-protein-evolution-design-and-adaptation</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/description-atomic-burials-compact-globular-proteins-fermi-dirac-probability</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/understanding-ensemble-protein-folding-atomic-detail</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/divergent-evolution-structural-proteome-phenomenological-models</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/common-motifs-and-topological-effects-protein-folding-transition-state</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/semiconservative-quasispecies-equations-polysomic-genomes-haploid-case</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/identification-minimal-protein-folding-nucleus-through-loop-entropy-perturbations</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/physical-origins-protein-superfamilies</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/pdb-uf-database-predicted-enzymatic-functions-unannotated-protein-structures-structural</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/folding-and-binding-conformational-repertoire-proteins-folding-aggregation-and</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/genetic-instability-and-quasispecies-model</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/simple-physical-model-scaling-protein-protein-interaction-networks</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/high-resolution-protein-folding-transferable-potential</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/entropic-stabilization-proteins-and-its-proteomic-consequences</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/geometric-and-physical-considerations-realistic-protein-models</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/physics-and-evolution-thermophilic-adaptation</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/predicting-specificity-determining-residues-two-large-eukaryotic-transcription-factor</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/lessons-design-novel-atomic-potential-protein-folding</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/reconstruction-src-sh3-protein-domain-transition-state-ensemble-using-multiscale</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/evolutionary-dynamics-adult-stem-cells-comparison-random-and-immortal-strand</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/selective-advantage-conservative-viruses</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/nucleation-and-transition-state-sh3-domain</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/emergence-scaling-sequence-based-physical-models-protein-evolution</loc>
  <lastmod>2025-05-15T18:57:02+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/determining-functional-specificity-protein-sequences</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/coc-database-universally-conserved-residues-protein-folds</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/prokaryotic-phylogenies-inferred-protein-structural-domains</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/imperfect-dna-lesion-repair-semiconservative-quasispecies-model-derivation-hamming</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/importance-dna-repair-tumor-suppression</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/all-atom-monte-carlo-simulation-gcaa-rna-folding</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/solution-quasispecies-model-arbitrary-gene-network</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/solvation-versus-freezing-heteropolymer-globule</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/native-atom-types-knowledge-based-potentials-application-binding-energy-prediction</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/evolution-dynamics-model-proteins</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/semiconservative-replication-quasispecies-model</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/host-parasite-coevolution-and-optimal-mutation-rates-semiconservative-quasispecies</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/structural-mining-self-consistent-design-flexible-protein-peptide-docking-and</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/simulation-experiment-and-evolution-understanding-nucleation-protein-s6-folding</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/commitment-and-nucleation-protein-g-transition-state</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/proteomic-traces-speciation</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/error-and-repair-catastrophes-two-dimensional-phase-diagram-quasispecies-model</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/imprint-evolution-protein-structures</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/identifying-importance-amino-acids-protein-folding-crystal-structures</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-evolution-within-structural-space</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/equilibrium-distribution-mutators-single-fitness-peak-model</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/using-protein-design-homology-detection-and-active-site-searches</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/natural-selection-more-designable-folds-mechanism-thermophilic-adaptation</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/side-chain-dynamics-and-protein-folding</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/structural-determinant-protein-designability</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/fold-recognition-minimal-gaps</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/amino-acids-determining-enzyme-substrate-specificity-prokaryotic-and-eukaryotic-protein</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/functional-fingerprints-folds-evidence-correlated-structure-function-evolution</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/direct-molecular-dynamics-observation-protein-folding-transition-state-ensemble</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/molecular-dynamics-simulation-sh3-domain-aggregation-suggests-generic-amyloidogenesis</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/glassy-dynamics-side-chain-ordering-simple-model-protein-folding</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/expanding-protein-universe-and-its-origin-biological-big-bang</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/phase-diagram-unzipping-dna-long-range-interactions</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/ensemble-folding-kinetics-protein-g-all-atom-monte-carlo-simulation</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/topological-determinants-protein-folding</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/small-molecule-growth-2001-smog2001-improved-knowledge-based-scoring-function-protein</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/reversible-stretching-random-heteropolymers</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/thermodynamics-and-folding-kinetics-analysis-sh3-domain-form-discrete-molecular</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/knowledge-based-potentials-combinatorial-lead-design-silico</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/structure-based-method-derivation-all-atom-potentials-protein-folding</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/combinatorial-computational-method-gives-new-picomolar-ligands-known-enzyme</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/constructing-verifying-and-dissecting-folding-transition-state-chymotrypsin-inhibitor-2</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/understanding-hierarchical-protein-evolution-first-principles</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/excluded-volume-protein-side-chain-packing</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/characterization-folding-kinetics-three-helix-bundle-protein-minimalist-langevin-model</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/energy-profile-space-model-protein-sequences</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/mode-coupling-theory-heteropolymers</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/folding-thermodynamics-and-kinetics-crambin-using-all-atom-monte-carlo-simulation</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/different-circular-permutations-produced-different-folding-nuclei-proteins</loc>
  <lastmod>2025-05-15T18:57:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/proteins-selected-sequences-heteropolymeric-study</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/differential-stabilization-two-hydrophobic-cores-transition-state-villin-14t-folding</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/comparison-two-optimization-methods-derive-energy-parameters-protein-folding-perceptron</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/statistical-significance-protein-structure-prediction-threading</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/what-can-disulfide-bonds-tell-us-about-protein-energetics-function-and-folding</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/analysis-knowledge-based-protein-ligand-potentials-using-self-consistent-method</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/kinetics-thermodynamics-and-evolution-non-native-interactions-protein-folding-nucleus</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/hiking-energy-landscape-sequence-space-bumpy-road-good-folders</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/when-and-how-can-homologs-overcome-errors-energy-estimates-and-make-3d-structure</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/identifying-protein-folding-nucleus-using-molecular-dynamics</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/modeling-kinetics-acylation-insulin-using-recursive-method-solving-systems-coupled</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/evidence-role-prpc-helix-1-hydrophilic-seeding-prion-aggregates</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/universally-conserved-positions-protein-folds-reading-evolutionary-signals-about</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/folding-association</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/folding-nucleus-specific-or-multiple-insights-lattice-models-and-experiments</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/discrete-molecular-dynamics-studies-folding-protein-model</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/folding-kinetics-villin-14t-protein-domain-central-beta-sheet-and-two-hydrophobic-cores</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-structure-prediction-threading-why-it-works-and-why-it-does-not</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-design-perspective-simple-tractable-models</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-folding-think-globally-interact-locally</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-design-perspective-simple-tractable-models-0</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-engineering-analysis-transition-state-protein-folding-simulation-lattice-model</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/theory-kinetic-partitioning-protein-folding-possible-applications-prions</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/how-evolution-makes-proteins-fold-quickly</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/theoretical-studies-protein-folding-thermodynamics-and-kinetics</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/computer-simulations-prebiotic-evolution</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/chain-length-scaling-protein-folding-time</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/how-derive-protein-folding-potential-new-approach-old-problem</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/dynamics-heteropolymers-dilute-solution-effective-equation-motion-and-relaxation</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/adsorption-freezing-transition-random-heteropolymers-near-disordered-2d-manifolds-due</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/frozen-phases-random-heteropolymers-disordered-media</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/how-first-biopolymers-could-have-evolved</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/simulations-chaperone-assisted-folding</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/design-proteins-selected-thermal-properties</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/improved-design-stable-and-fast-folding-model-proteins</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/modeling-protein-folding-beauty-and-power-simplicity</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/universality-and-diversity-protein-folding-scenarios-comprehensive-analysis-aid-lattice</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/impact-local-and-non-local-interactions-thermodynamics-and-kinetics-protein-folding</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/exhaustive-enumeration-protein-conformations-using-experimental-restraints</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/domains-folding-model-proteins</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/critical-compositions-microphase-separation-transition-random-copolymers</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/burst-hydrophobic-collapse-necessary-protein-folding</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/evolution-selection-fast-folding-model-proteins</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/test-lattice-protein-folding-algorithms</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/effect-net-charge-conformation-polyampholytes</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/phase-transitions-many-letter-random-heteropolymer</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/pseudodihedrals-simplified-protein-backbone-representation-knowledge-based-energy</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/specific-nucleus-transition-state-protein-folding-evidence-lattice-model</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/proteins-selected-sequences-fold-unique-native-conformation</loc>
  <lastmod>2025-05-15T19:01:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/phase-transitions-heteropolymers-secondary-structure</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/new-approach-design-stable-proteins</loc>
  <lastmod>2025-05-15T18:57:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/engineering-stable-and-fast-folding-sequences-model-proteins</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/phase-diagram-random-copolymers</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/influence-point-mutations-protein-structure-probability-neutral-mutation</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/activation-energy-landscape-metastable-rna-folding</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/implications-thermodynamics-protein-folding-evolution-primary-sequences</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/formation-unique-structure-polypeptide-chains-theoretical-investigation-aid-replica</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/theory-cooperative-transitions-protein-molecules-ii-phase-diagram-protein-molecule</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/theory-cooperative-transitions-protein-molecules-i-why-denaturation-globular-protein</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/role-topological-limitations-kinetics-homopolymer-collapse-and-self-assembly</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/solid-interactions-statistical-physics-biopolymers</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/theory-heteropolymers-frozen-random-primary-structure-properties-globular-state-coil</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/fluctuating-state-protein-globule</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/protein-globule-without-unique-three-dimensional-structure-experimental-data-alpha</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/theory-cooperative-transitions-protein-globules</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/theory-dna-compactization-polymer-solution</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/dna-compaction-diluted-polymeric-solutions</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publication/fusion-heteropolymeric-chains-case-which-energy-cooperativity-depends-type-boundaries</loc>
  <lastmod>2025-05-15T18:57:14+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/news/new-website</loc>
  <lastmod>2013-09-15T01:27:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/news/open-house</loc>
  <lastmod>2013-10-15T18:44:13+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-bharat</loc>
  <lastmod>2013-09-13T18:10:22+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-adrian</loc>
  <lastmod>2013-09-13T18:11:08+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-shimon</loc>
  <lastmod>2013-09-13T18:13:33+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-ariel</loc>
  <lastmod>2013-10-08T17:52:03+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-orit</loc>
  <lastmod>2013-10-08T17:51:48+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-murat</loc>
  <lastmod>2013-09-13T18:13:05+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/open-house</loc>
  <lastmod>2013-10-15T18:40:12+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-orit-0</loc>
  <lastmod>2013-10-15T18:42:31+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-sanchari</loc>
  <lastmod>2013-10-15T18:42:45+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-nicolas</loc>
  <lastmod>2013-12-02T15:19:10+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-jeong-mo</loc>
  <lastmod>2014-01-13T16:45:51+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-michael-manhart-guest-speaker</loc>
  <lastmod>2013-11-11T23:04:45+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-fahimeh-baftizadeh</loc>
  <lastmod>2013-12-02T15:20:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/gm-adrian</loc>
  <lastmod>2014-01-13T16:46:09+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-jaie</loc>
  <lastmod>2014-01-26T20:13:12+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-amy</loc>
  <lastmod>2014-01-26T20:13:54+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/event/group-meeting-ariel-0</loc>
  <lastmod>2014-01-26T20:14:34+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people</loc>
  <lastmod>2025-01-28T15:00:25+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/publications</loc>
  <lastmod>2025-01-28T15:05:59+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/software</loc>
  <lastmod>2025-02-04T17:46:34+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links</loc>
  <lastmod>2025-02-04T17:48:29+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/calendar</loc>
  <lastmod>2025-02-04T18:17:40+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/calendar/past_events</loc>
  <lastmod>2025-02-04T18:18:17+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/shakhnovich-biophysics-lab</loc>
  <lastmod>2025-11-19T03:43:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/theoretical-molecular-evolution</loc>
  <lastmod>2025-02-04T17:43:48+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/experimental-lab</loc>
  <lastmod>2025-02-04T17:42:52+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/drug-discovery</loc>
  <lastmod>2025-02-04T17:44:48+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/protein-folding-and-design</loc>
  <lastmod>2025-02-04T17:45:50+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/lab-alumni</loc>
  <lastmod>2025-01-28T15:05:09+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/contact-us</loc>
  <lastmod>2025-02-04T17:50:36+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/protein-folding</loc>
  <lastmod>2013-10-16T18:38:20+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/book-chapters</loc>
  <lastmod>2025-02-04T17:38:43+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/publications-1979-1989</loc>
  <lastmod>2025-01-28T15:12:32+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/publications-1990-1999</loc>
  <lastmod>2025-05-16T03:06:03+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/research</loc>
  <lastmod>2025-05-22T20:57:16+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/decoyang-shakhnovich</loc>
  <lastmod>2013-10-21T15:17:03+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/transition-state-ensemble</loc>
  <lastmod>2013-10-21T15:15:32+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/sdr</loc>
  <lastmod>2013-10-15T21:53:46+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/pdb-uf</loc>
  <lastmod>2025-01-29T14:58:42+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/group-photo</loc>
  <lastmod>2025-03-25T03:50:30+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/funding</loc>
  <lastmod>2025-01-28T17:03:41+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/cotrans-rates</loc>
  <lastmod>2020-01-13T14:50:37+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/software/coarse-grained-co-translational-folding-analysis</loc>
  <lastmod>2025-02-04T17:54:16+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/software/minimalistic-predictor-protein-binding-energy</loc>
  <lastmod>2025-01-28T17:01:31+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/software/monte-carlo-protein-unfolding-mcpu</loc>
  <lastmod>2025-01-28T17:01:19+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/software/opengrowth</loc>
  <lastmod>2025-01-28T17:00:58+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/software/protein-domain-swapping-model</loc>
  <lastmod>2025-01-28T17:00:38+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/pages/prediction-viral-evolution-biophysics-and-machine-learning</loc>
  <lastmod>2025-05-22T20:58:24+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/eugene-shakhnovich</loc>
  <lastmod>2025-05-15T18:40:30+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/dwipanjan-sanyal</loc>
  <lastmod>2025-05-17T19:54:16+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/kibum-park</loc>
  <lastmod>2021-07-06T14:27:20+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/junlang-liu</loc>
  <lastmod>2024-03-09T01:24:00+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/john-dianzhuo-wang</loc>
  <lastmod>2023-08-07T20:08:45+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/aniruddha-chattaraj</loc>
  <lastmod>2022-09-22T16:45:10+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/marian-huot</loc>
  <lastmod>2025-05-17T19:51:26+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/vaibhav-mohanty</loc>
  <lastmod>2025-04-04T04:05:11+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/sayantan-mondal</loc>
  <lastmod>2024-03-09T01:23:20+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/arthur-bigot</loc>
  <lastmod>2026-04-06T23:07:08+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/antoine-maechler</loc>
  <lastmod>2025-05-15T18:46:05+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/zhouyu-zhang</loc>
  <lastmod>2024-07-24T18:52:07+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/qianxiang-xu</loc>
  <lastmod>2024-07-24T18:58:36+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/jio-jeong</loc>
  <lastmod>2024-08-19T21:06:42+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/jonathan-feldman</loc>
  <lastmod>2025-07-04T04:36:40+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/people/saadi-el-saadi</loc>
  <lastmod>2025-10-07T20:51:04+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/httpwwwrcsborgpdbhomehomedo</loc>
  <lastmod>2025-01-28T17:10:40+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/condensed-matter-theory-harvard</loc>
  <lastmod>2025-01-28T17:10:24+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/database-transition-state-ensemble</loc>
  <lastmod>2025-01-28T17:08:57+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/database-decoyang-shakhnovich</loc>
  <lastmod>2025-01-28T17:08:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/protein-folding</loc>
  <lastmod>2025-01-28T17:10:06+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/database-sdr</loc>
  <lastmod>2025-01-28T17:08:20+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/database-pdb-uf</loc>
  <lastmod>2025-01-29T14:59:04+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/coc</loc>
  <lastmod>2025-02-04T17:48:03+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/group-wiki</loc>
  <lastmod>2025-01-28T17:09:46+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/proteomevis</loc>
  <lastmod>2025-01-28T17:09:32+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/links/database-co-translational-folding-rates-nonnative-interactions</loc>
  <lastmod>2025-01-28T17:09:17+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/resource/opengrowthmanualpdf</loc>
  <lastmod>2025-01-27T09:27:27+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/resource/opengrowthmanualpdf-0</loc>
  <lastmod>2025-01-27T09:27:27+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/resource/opengrowthmanual041pdf</loc>
  <lastmod>2025-01-27T09:27:27+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/news-categories/news</loc>
  <lastmod>2025-01-27T09:27:15+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/news-categories/blog</loc>
  <lastmod>2025-01-27T09:27:15+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/page-categories/software</loc>
  <lastmod>2025-01-28T15:49:35+00:00</lastmod>
  <priority>0.5</priority>
 </url>
 <url>
  <loc>https://shakhnovich.faculty.chemistry.harvard.edu/taxonomy/term/11</loc>
  <lastmod>2025-01-28T17:07:28+00:00</lastmod>
  <priority>0.5</priority>
 </url>
</urlset>
