For publications after 2000, please click here.

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