# Publications 1990-1999 For publications after 2000, please click on 'Publications' in the main menu. Finkelstein AV, Rykunov DS, Lobanov MY, Mirny LA, **Shakhnovich EI**. When and how the homologs can overcome errors in the energy estimates and make the 3D structure prediction possible BIOFIZIKA+ 44 (6): 980-991 NOV-DEC 1999 Du R, Pande VS, Grosberg AY, Tanaka T, **Shakhnovich EI** On the role of conformational geometry in protein folding J CHEM PHYS 111 (22): 10375-10380 DEC 8 1999 Kussell EL, **Shakhnovich EI** Analytical approach to the protein design problem PHYS REV LETT 83 (21): 4437-4440 NOV 22 1999 Morrissey MP, **Shakhnovich EI** Evidence for the role of PrPC helix 1 in the hydrophilic seeding of prion aggregates P NATL ACAD SCI USA 96 (20): 11293-11298 SEP 28 1999 Mirny LA, **Shakhnovich EI** Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function J MOL BIOL 291 (1): 177-196 AUG 6 1999 Angerman HJ, **Shakhnovich E** Freezing in polyampholytes globules: Influence of the long-range nature of the interaction J CHEM PHYS 111 (2): 772-785 JUL 8 1999 Berriz GF, **Shakhnovich EI** The well-tempered protein CURR OPIN COLLOID IN 4 (1): 72-82 FEB 1999 Broglia RA, Tiana G, Roman HE, **Shakhnovich EI.** Stability of designed proteins against mutations PHYS REV LETT 82 (23): 4727-4730 JUN 7 1999 Gutman L, **Shakhnovich E** Disordered heteropolymers with cross-links - phase diagram and conformational transitions CHEM PHYS LETT 303 (3-4): 355-362 APR 9 1999 Qi SY, Chakraborty AK, Wang H, Lefebre AA, Balsara NP, Shakhnovich EI, Xeridou M., Hadjichristis N. Microphase ordering in melts of randomly grafted copolymers PHYS REV LETT 82 (14): 2896-2899 APR 5 1999 Michnick SW, **Shakhnovich E** A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies FOLD DES 3 (4): 239-251 1998 Gutman L, **Shakhnovich E** Phase diagram analysis of random heteropolymers with composition specific and quenched cross-links J CHEM PHYS 109 (7): 2947-2958 AUG 15 1998 Bratko D, Chakraborty AK, **Shakhnovich EI** Adsorption of random copolymers on disordered surfaces COMPUT THEOR POLYM S 8 (1-2): 113-126 Part 2 Sp. Iss. SI 1998 Fersht AR, **Shakhnovich EI** Protein folding: Think globally, (inter)act locally CURR BIOL 8 (14): R478-R479 JUL 2 1998 Mammen M, **Shakhnovich EI**, Deutch JM, Whitesides GW Estimating the entropic cost of self-assembly of multiparticle hydrogen-bonded aggregates based on the cyanuric acid center dot melamine lattice J ORG CHEM 63 (12): 3821-3830 JUN 12 1998 **Shakhnovich EI** Protein design: a perspective from simple tractable models FOLD DES 3 (3): R45-R58 1998 Gutin AM, Abkevich VI, **Shakhnovich EI** A protein engineering analysis of the transition state for protein folding: simulation in the lattice model FOLD DES 3 (3): 183-194 1998 Abkevich VI, Gutin AM, **Shakhnovich EI** Theory of kinetic partitioning in protein folding with possible applications to prions PROTEINS 31 (4): 335-344 JUN 1 1998 Mammen M, **Shakhnovich EI**, Whitesides GM Using a convenient, quantitative model for torsional entropy to establish qualitative trends for molecular processes that restrict conformational freedom J ORG CHEM 63 (10): 3168-3175 MAY 15 1998 Mirny LA, Abkevich VI, **Shakhnovich EI** How evolution makes proteins fold quickly P NATL ACAD SCI USA 95 (9): 4976-4981 APR 28 1998 Chou JJ, **Shakhnovich EI** A study on local-global cooperativity in protein collapse J PHYS CHEM B 103 (13): 2535-2542 APR 1 1999 Dinner AR, Abkevich V, **Shakhnovich E**, Karplus, M. Factors that affect the folding ability of proteins PROTEINS 35 (1): 34-40 APR 1 1999 Roan JR, **Shakhnovich EI** Phase separation of a binary fluid containing surfactants in a Hele-Shaw cell PHYS REV E 59 (2): 2109-2125 Part B FEB 1999 **Shakhnovich EI** Folding by association NAT STRUCT BIOL 6 (2): 99-102 FEB 1999 **Shakhnovich EI** Folding nucleus: specific or multiple? Insights from lattice models and experiments FOLD DES 3 (6): R108-R111 1998 Dokholyan NV, Buldyrev SV, Stanley HE, **Shakhnovich EI**. Discrete molecular dynamics studies of the folding of a protein-like model FOLD DES 3 (6): 577-587 1998 Roan JR, **Shakhnovich EI** Stability study of icosahedral phases in diblock copolymer melt J CHEM PHYS 109 (17): 7591-7611 NOV 1 1998 Mirny LA, **Shakhnovich EI** Protein structure prediction by threading. Why it works and why it does not J MOL BIOL 283 (2): 507-526 OCT 23 1998 Choe SE, Matsudaira PT, Osterhout J, Wagner G, **Shakhnovich EI**. Folding kinetics of villin 14T, a protein domain with a central beta-sheet and two hydrophobic cores BIOCHEMISTRY-US 37 (41): 14508-14518 OCT 13 1998 Gutin A, Sali A, Abkevich V, Karplus M, **Shakhnovich EI** Temperature dependence of the folding rate in a simple protein model: Search for a "glass" transition J CHEM PHYS 108 (15): 6466-6483 APR 15 1998 **Shakhnovich E**, Fersht AR Folding and binding - overview CURR OPIN STRUC BIOL 8 (1): 65-67 FEB 1998 Chakraborty AK, **Shakhnovich EI**, Pande VS Freezing of compact random heteropolymers with correlated sequence fluctuations J CHEM PHYS 108 (4): 1683-1687 JAN 22 1998 Gutin A, Abkevich V, **Shakhnovich E** Comment on "Chain length scaling of protein folding time" - Reply PHYS REV LETT 80 (1): 208-208 JAN 5 1998 Du R, Pande VS, Grosberg AY, Tanaka T, **Shakhnovich EI**. On the transition coordinate for protein folding J CHEM PHYS 108 (1): 334-350 JAN 1 1998 Tiana G, Broglia RA, Roman HE, et al. Folding and misfolding of designed proteinlike chains with mutations J CHEM PHYS 108 (2): 757-761 JAN 8 1998 Bratko D, Chakraborty AK, **Shakhnovich EI** Recognition between random heteropolymers and multifunctional disordered surfaces CHEM PHYS LETT 280 (1-2): 46-52 NOV 28 1997 Chakraborty AK, **Shakhnovich EI** Polymer adsorption on disordered substrates - Reply PHYS REV LETT 79 (24): 4931-4931 DEC 15 1997 Sfatos CD, **Shakhnovich EI** Statistical mechanics of random heteropolymers PHYS REP 288 (1-6): 77-108 SEP 1997 DeWitte RS, **Shakhnovich E** SMoG: De novo design method based on simple, fast and accurate free energy estimates. ABSTR PAP AM CHEM S 214: 6-COMP Part 1 SEP 7 1997 Gutman L, **Shakhnovich E** Frozen phases with re-entrant transition for random heteropolymers with composition specific and annealed cross-links J CHEM PHYS 107 (4): 1247-1258 JUL 22 1997 Berriz GF, Gutin AM, **Shakhnovich EI** Cooperativity and stability in a Langevin model of proteinlike folding J CHEM PHYS 106 (22): 9276-9285 JUN 8 1997 **Shakhnovich EI** Unravelling mechanisms of protein folding, evolution and design. ABSTR PAP AM CHEM S 213: 63-COMP Part 1 APR 13 1997 **Shakhnovich EI** Theoretical studies of protein-folding thermodynamics and kinetics CURR OPIN STRUC BIOL 7 (1): 29-40 FEB 1997 Bratko D, Chakraborty AK, **Shakhnovich EI** The structure of a random heteropolymer in a disordered medium: Ensemble growth simulation J CHEM PHYS 106 (3): 1264-1279 JAN 15 1997 Mirny LA, Abkevich V, **Shakhnovich EI** Universality and diversity of the protein folding scenarios: A comprehensive analysis with the aid of a lattice model FOLD DES 1 (2): 103-116 1996 Morrissey MP, **Shakhnovich EI** Design of proteins with selected thermal properties FOLD DES 1 (5): 391-405 1996 **Shakhnovich EI** Modeling protein folding: The beauty and power of simplicity FOLD DES 1 (3): R50-R54 1996 Abkevich VI, Gutin AM, **Shakhnovich EI** Improved design of stable and fast-folding model proteins FOLD DES 1 (3): 221-230 1996 Gutin AM, Abkevich VI, **Shakhnovich EI** Chain length scaling of protein folding time PHYS REV LETT 77 (27): 5433-5436 DEC 30 1996 Mirny LA, **Shakhnovich EI** How to derive a protein folding potential? A new approach to an old problem J MOL BIOL 264 (5): 1164-1179 DEC 20 1996 Roan JR, **Shakhnovich EI** Dynamics of heteropolymers in dilute solution: Effective equation of motion and relaxation spectrum PHYS REV E 54 (5): 5340-5357 NOV 1996 Srebnik S, Chakraborty AK, **Shakhnovich EI** Adsorption-freezing transition for random heteropolymers near disordered 2D manifolds due to ''pattern matching'' PHYS REV LETT 77 (15): 3157-3160 OCT 7 1996 Bratko D, Chakraborty AK, **Shakhnovich EI** Frozen phases of random heteropolymers in disordered media PHYS REV LETT 76 (11): 1844-1847 MAR 11 1996 Abkevich VI, Gutin AM, **Shakhnovich EI** How the first biopolymers could have evolved P NATL ACAD SCI USA 93 (2): 839-844 JAN 23 1996 Sfatos CD, Gutin AM, Abkevich VI, Shakhnovich EI. Simulations of chaperone-assisted folding BIOCHEMISTRY-US 35 (1): 334-339 JAN 9 1996 **Shakhnovich E**, Abkevich V, Ptitsyn O Conserved residues and the mechanism of protein folding NATURE 379 (6560): 96-98 JAN 4 1996 Chakraborty AK, **Shakhnovich EI** Phase behavior of random copolymers in quenched random media J CHEM PHYS 103 (24): 10751-10763 DEC 22 1995 DEWITTE RS, MICHNICK SW, **Shakhnovich EI** EXHAUSTIVE ENUMERATION OF PROTEIN CONFORMATIONS USING EXPERIMENTAL RESTRAINTS PROTEIN SCI 4 (9): 1780-1791 SEP 1995 ABKEVICH VI, GUTIN AM, **Shakhnovich EI** IMPACT OF LOCAL AND NONLOCAL INTERACTIONS ON THERMODYNAMICS AND KINETICS OF PROTEIN-FOLDING J MOL BIOL 252 (4): 460-471 SEP 29 1995 **Shakhnovich EI** STATISTICAL-MECHANICS OF IN-VITRO AND IN-VIVO PROTEIN ABSTR PAP AM CHEM S 210: 95-PHYS Part 2 AUG 20 1995 MA JP, STRAUB JE, **Shakhnovich EI** SIMULATION STUDY OF THE COLLAPSE OF LINEAR AND RING HOMOPOLYMERS J CHEM PHYS 103 (7): 2615-2624 AUG 15 1995 ABKEVICH VI, GUTIN AM, **Shakhnovich EI** DOMAINS IN FOLDING OF MODEL PROTEINS PROTEIN SCI 4 (6): 1167-1177 JUN 1995 SFATOS CD, GUTIN AM, **Shakhnovich EI** CRITICAL COMPOSITIONS IN THE MICROPHASE SEPARATION TRANSITION OF RANDOM COPOLYMERS PHYS REV E 51 (5): 4727-4734 Part B MAY 1995 GROSBERG A, GUTIN A, **Shakhnovich E** CONFORMATIONAL ENTROPY OF A BRANCHED POLYMER MACROMOLECULES 28 (10): 3718-3727 MAY 8 1995 **Shakhnovich EI** STATISTICAL-MECHANICS OF PROTEIN-FOLDING AND EVOLUTION FASEB J 9 (6): A1239-A1239 APR 24 1995 SFATOS CD, GUTIN AM, **Shakhnovich EI** FREEZING AND MICROPHASE SEPARATION IN RANDOM COPOLYMERS NUOVO CIMENTO D 16 (7): 873-877 JUL 1994 SFATOS CD, GUTIN AM, **Shakhnovich EI** FLUCTUATION EFFECTS ON MICROPHASE SEPARATION IN RANDOM COPOLYMERS NUOVO CIMENTO D 16 (7): 879-882 JUL 1994 **Shakhnovich EI** PROTEINS WITH SELECTED SEQUENCES FOLD INTO UNIQUE NATIVE CONFORMATION (VOL 72, PG 3907, 1994) PHYS REV LETT 74 (13): 2618-2618 MAR 27 1995 GUTIN AM, ABKEVICH VI, **Shakhnovich EI** IS BURST HYDROPHOBIC COLLAPSE NECESSARY FOR PROTEIN-FOLDING BIOCHEMISTRY-US 34 (9): 3066-3076 MAR 7 1995 GUTIN AM, ABKEVICH VI, **Shakhnovich EI** EVOLUTION-LIKE SELECTION OF FAST-FOLDING MODEL PROTEINS P NATL ACAD SCI USA 92 (5): 1282-1286 FEB 28 1995 KARPLUS M, SALI A, **Shakhnovich E** KINETICS OF PROTEIN-FOLDING - REPLY NATURE 373 (6516): 665-665 FEB 23 1995 YUE K, FIEBIG KM, THOMAS PD, et al. A TEST OF LATTICE PROTEIN-FOLDING ALGORITHMS P NATL ACAD SCI USA 92 (1): 325-329 JAN 3 1995 GUTIN AM, SFATOS CD, **Shakhnovich EI** FLUCTUATION EFFECTS ON MICROPHASE SEPARATION IN RANDOM COPOLYMERS J PHYS A-MATH GEN 27 (24): 7957-7968 DEC 21 1994 GUTIN AM, **Shakhnovich EI** EFFECT OF A NET CHARGE ON THE CONFORMATION OF POLYAMPHOLYTES PHYS REV E 50 (5): R3322-R3325 NOV 1994 SFATOS CD, GUTIN AM, **Shakhnovich EI** PHASE-TRANSITIONS IN A MANY-LETTER RANDOM HETEROPOLYMER PHYS REV E 50 (4): 2898-2905 OCT 1994 DEWITTE RS, **Shakhnovich EI** PSEUDODIHEDRALS - SIMPLIFIED PROTEIN BACKBONE REPRESENTATION WITH KNOWLEDGE-BASED ENERGY PROTEIN SCI 3 (9): 1570-1581 SEP 1994 ABKEVICH VI, GUTIN AM, **Shakhnovich EI** FREE-ENERGY LANDSCAPE FOR PROTEIN-FOLDING KINETICS - INTERMEDIATES, TRAPS, AND MULTIPLE PATHWAYS IN THEORY AND LATTICE MODEL SIMULATIONS J CHEM PHYS 101 (7): 6052-6062 OCT 1 1994 RAMANATHAN S, **Shakhnovich E** STATISTICAL-MECHANICS OF PROTEINS WITH EVOLUTIONARY SELECTED SEQUENCES PHYS REV E 50 (2): 1303-1312 Part A AUG 1994 ABKEVICH VI, GUTIN AM, **Shakhnovich EI** SPECIFIC NUCLEUS AS THE TRANSITION-STATE FOR PROTEIN-FOLDING - EVIDENCE FROM THE LATTICE MODEL BIOCHEMISTRY-US 33 (33): 10026-10036 AUG 23 1994 DINNER A, SALI A, KARPLUS M, et al. PHASE-DIAGRAM OF A MODEL PROTEIN-DERIVED BY EXHAUSTIVE ENUMERATION OF THE CONFORMATIONS J CHEM PHYS 101 (2): 1444-1451 JUL 15 1994 SFATOS CD, GUTIN AM, **Shakhnovich EI** FLUCTUATION EFFECTS ON MICROPHASE SEPARATION IN A RANDOM COPOLYMER HAMILTONIAN J PHYS A-MATH GEN 27 (12): L411-L416 JUN 21 1994 **Shakhnovich EI** PROTEINS WITH SELECTED SEQUENCES FOLD INTO UNIQUE NATIVE CONFORMATION PHYS REV LETT 72 (24): 3907-3910 JUN 13 1994 GUTIN AM, **Shakhnovich EI** STATISTICAL-MECHANICS OF POLYMERS WITH DISTANCE CONSTRAINTS J CHEM PHYS 100 (7): 5290-5293 APR 1 1994 SALI A, **Shakhnovich E**, KARPLUS M HOW DOES A PROTEIN FOLD NATURE 369 (6477): 248-251 MAY 19 1994 ARCHONTIS GZ, **Shakhnovich EI** PHASE-TRANSITIONS IN HETEROPOLYMERS WITH SECONDARY STRUCTURE PHYS REV E 49 (4): 3109-3123 Part A APR 1994 DEWITTE RS, **Shakhnovich EI** PSEUDODIHEDRALS - SIMPLIFIED BACKBONE REPRESENTATION WITH KNOWLEDGE-BASED ENERGY BIOPHYS J 66 (2): A395-A395 Part 2 FEB 1994 SALI A, **Shakhnovich E**, KARPLUS M KINETICS OF PROTEIN-FOLDING - A LATTICE MODEL STUDY OF THE REQUIREMENTS FOR FOLDING TO THE NATIVE-STATE J MOL BIOL 235 (5): 1614-1636 FEB 4 1994 **Shakhnovich EI**, GUTIN AM A NEW APPROACH TO THE DESIGN OF STABLE PROTEINS PROTEIN ENG 6 (8): 793-800 NOV 1993 **Shakhnovich EI**, GUTIN AM ENGINEERING OF STABLE AND FAST-FOLDING SEQUENCES OF MODEL PROTEINS P NATL ACAD SCI USA 90 (15): 7195-7199 AUG 1 1993 **Shakhnovich E** PROTEIN-FOLDING - LESSONS FOR PROTEIN DESIGN ABSTR PAP AM CHEM S 206: 98-PHYS Part 2 AUG 22 1993 SFATOS CD, GUTIN AM, **Shakhnovich EI** PHASE-DIAGRAM OF RANDOM COPOLYMERS PHYS REV E 48 (1): 465-475 JUL 1993 GUTIN AM, GROSBERG AY, **Shakhnovich EI** MICROPHASE SEPARATION IN RANDOMLY BRANCHED POLYMERS MACROMOLECULES 26 (14): 3598-3600 JUL 5 1993 GUTIN AM, **Shakhnovich EI** GROUND-STATE OF RANDOM COPOLYMERS AND THE DISCRETE RANDOM ENERGY-MODEL J CHEM PHYS 98 (10): 8174-8177 MAY 15 1993 GUTIN AM, GROSBERG AY, **Shakhnovich EI** POLYMERS WITH ANNEALED AND QUENCHED BRANCHINGS BELONG TO DIFFERENT UNIVERSALITY CLASSES MACROMOLECULES 26 (6): 1293-1295 MAR 15 1993 GUTIN AM, GROSBERG AY, **Shakhnovich EI** GLOBULAR STATE OF BRANCHED RANDOM HETEROPOLYMERS J PHYS A-MATH GEN 26 (5): 1037-1049 MAR 7 1993 **Shakhnovich E** STATISTICAL-MECHANICS OF PROTEIN FOLDING BIOPHYS J 64 (2): A245-A245 Part 2 FEB 1993 **Shakhnovich E**, FARZTDINOV G, GUTIN AM, Karplus M.. PROTEIN FOLDING BOTTLENECKS - A LATTICE MONTE-CARLO SIMULATION PHYS REV LETT 67 (12): 1665-1668 SEP 16 1991 **Shakhnovich EI**, GUTIN AM INFLUENCE OF POINT MUTATIONS ON PROTEIN-STRUCTURE - PROBABILITY OF AF A NEUTRAL MUTATION J THEOR BIOL 149 (4): 537-546 APR 21 1991 **Shakhnovich E**, GUTIN A ENUMERATION OF ALL COMPACT CONFORMATIONS OF COPOLYMERS WITH RANDOM SEQUENCE OF LINKS J CHEM PHYS 93 (8): 5967-5971 OCT 15 1990 FERNANDEZ A, **Shakhnovich EI** ACTIVATION-ENERGY LANDSCAPE FOR METASTABLE RNA FOLDING PHYS REV A 42 (6): 3657-3659 SEP 15 1990 **Shakhnovich EI**, GUTIN AM IMPLICATIONS OF THERMODYNAMICS OF PROTEIN FOLDING FOR EVOLUTION OF PRIMARY SEQUENCES NATURE 346 (6286): 773-775 AUG 23 1990 GAREL T, ORLAND H, **Shakhnovich EI** RANDOM HETEROPOLYMERS IN LAYERED FLUIDS J CHEM PHYS 93 (3): 2043-2047 AUG 1 1990