PUBLICATIONS: 1990-1999

[2000-2005]  |  [1990-1999]  |  [1979-1989]   |  [Book Chapters]

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

DeWitte RS, Ishchenko AV, Shakhnovich EI
SMoG: De novo design method based on simple, fast, and accurate free energy estimates .2. Case studies in molecular design
J AM CHEM SOC 119 (20): 4608-4617 MAY 21 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

DeWitte RS, Shakhnovich EI
SMoG: de Novo design method based on simple, fast, and accurate free energy estimates .1. Methodology and supporting evidence
J AM CHEM SOC 118 (47): 11733-11744 NOV 27 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