Protein design: a perspective from simple tractable models

Principles that Govern the Folding of Protein Chains

1973 • 6,771 citations

Protein Structure Comparison by Alignment of Distance Matrices

1993 • 3,989 citations

Spin Glass Theory and Beyond

1986 • 3,761 citations

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

1991 • 2,629 citations

Funnels, pathways, and the energy landscape of protein folding: A synthesis

1995 • 2,607 citations

Spin glasses and the statistical mechanics of protein folding.

1987 • 1,608 citations

Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

1985 • 1,570 citations

De Novo Protein Design: Fully Automated Sequence Selection

1997 • 1,129 citations

Calculation of conformational ensembles from potentials of mena force

1990 • 1,091 citations

The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding

1995 • 745 citations

Protein Design by Binary Patterning of Polar and Nonpolar Amino Acids

1993 • 737 citations

Emergence of Preferred Structures in a Simple Model of Protein Folding

1996 • 666 citations

STUDIES ON PROTEIN FOLDING, UNFOLDING AND FLUCTUATIONS BY COMPUTER SIMULATION

1975 • 658 citations

Kinetics of Protein Folding

1994 • 572 citations

Nucleation mechanisms in protein folding

1997 • 552 citations

Engineering of stable and fast-folding sequences of model proteins.

1993 • 543 citations

Specific Nucleus as the Transition State for Protein Folding: Evidence from the Lattice Model

1994 • 478 citations

Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications.

1995 • 467 citations

The role of topological constraints in the kinetics of collapse of macromolecules

1988 • 414 citations

Proteins with selected sequences fold into unique native conformation

1994 • 395 citations

Theoretical studies of protein-folding thermodynamics and kinetics

1997 • 387 citations

Conserved residues and the mechanism of protein folding

1996 • 347 citations

Optimal protein-folding codes from spin-glass theory.

1992 • 341 citations

Formation of unique structure in polypeptide chains

1989 • 319 citations

Functional rapidly folding proteins from simplified amino acid sequences

1997 • 306 citations

Protein folding bottlenecks: A lattice Monte Carlo simulation

1991 • 296 citations

A test of lattice protein folding algorithms.

1995 • 294 citations

Structure-derived potentials and protein simulations

1996 • 288 citations

Intermediate States in Protein Folding

1996 • 283 citations

How to Derive a Protein Folding Potential? A New Approach to an Old Problem

1996 • 282 citations

Implications of thermodynamics of protein folding for evolution of primary sequences

1990 • 279 citations

Impact of Local and Non-local Interactions on Thermodynamics and Kinetics of Protein Folding

1995 • 271 citations

SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence

1996 • 257 citations

Enumeration of all compact conformations of copolymers with random sequence of links

1990 • 256 citations

Pathways for protein folding: is a new view needed?

1998 • 254 citations

Probing the role of packing specificity in protein design

1997 • 252 citations

A new approach to the design of stable proteins

1993 • 240 citations

Chain Length Scaling of Protein Folding Time

1996 • 212 citations

The role of internal packing interactions in determining the structure and stability of a protein

1991 • 208 citations

Why do protein architectures have boltzmann‐like statistics?

1995 • 204 citations

Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations

1994 • 199 citations

Criterion that Determines the Foldability of Proteins

1996 • 198 citations

A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins

1993 • 196 citations

How evolution makes proteins fold quickly

1998 • 186 citations

Foldons, protein structural modules, and exons.

1996 • 172 citations

Is Burst Hydrophobic Collapse Necessary for Protein Folding?

1995 • 152 citations

All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination

1997 • 146 citations

Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein.

1994 • 144 citations

Potential energy functions for threading

1996 • 143 citations

Evolution-like selection of fast-folding model proteins.

1995 • 141 citations

New Algorithm for Protein Design

1996 • 131 citations

Statistical mechanics of simple models of protein folding and design

1997 • 130 citations

Optimal sequence selection in proteins of known structure by simulated evolution.

1994 • 130 citations

The Role of Backbone Flexibility in the Accommodation of Variants That Repack the Core of T4 Lysozyme

1993 • 122 citations

Phase diagram of random copolymers

1993 • 119 citations

Thermodynamics of protein folding: A statistical mechanical study of a small all-β protein

1997 • 110 citations

The crystal structure of a mutant protein with altered but improved hydrophobic core packing.

1994 • 110 citations

Universality and diversity of the protein folding scenarios:a comprehensive analysis with the aid of a lattice model

1996 • 109 citations

Nucleation mechanism for protein folding and theoretical predictions for hydrogen‐exchange labeling experiments

1995 • 94 citations

Optimal Protein Design Procedure

1996 • 92 citations

Why are the same protein folds used to perform different functions?

1993 • 91 citations

Thermodynamic procedure to synthesize heteropolymers that can renature to recognize a given target molecule.

1994 • 86 citations

Mean-field minimization methods for biological macromolecules

1996 • 84 citations

Statistical mechanics of proteins with ‘‘evolutionary selected’’ sequences

1994 • 77 citations

Searching for foldable protein structures using optimized energy functions

1995 • 77 citations

Temperature dependence of the folding rate in a simple protein model: Search for a “glass” transition

1998 • 77 citations

Improved design of stable and fast-folding model proteins

1996 • 76 citations

The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus

1997 • 76 citations

Ground state of random copolymers and the discrete random energy model

1993 • 75 citations

Design of proteins with selected thermal properties

1996 • 65 citations

Statistical Mechanics of the Combinatorial Synthesis and Analysis of Folding Macromolecules

1997 • 60 citations

Folding thermodynamics and kinetics of imprinted renaturable heteropolymers

1994 • 56 citations

Freezing transition of random heteropolymers consisting of an arbitrary set of monomers

1995 • 50 citations

Is Heteropolymer Freezing Well Described by the Random Energy Model?

1996 • 49 citations

Domains in folding of model proteins

1995 • 42 citations

Strain in the folding nucleus of chymotrypsin inhibitor 2

1997 • 33 citations

Statistical Mechanics of Macromolecules

2000 • 30 citations

Ribonucleotide reductase from Thermus X-1, a thermophilic organism

1973 • 27 citations

Effect of sequence and intermolecular interactions on the number and nature of low-energy states for simple model proteins

1993 • 21 citations

On constructing folding heteropolymers.

1995 • 16 citations

Theoretical approaches to designing novel sequences to fit a given fold

1995 • 7 citations

A free energy analysis by unfolding applied to 125-mers on a cubic lattice

1998 • 7 citations

Cooperativity of Protein Folding and the Random-Field Ising Model

1996 • 2 citations