Ab Initio Protein Structure Prediction: Progress and Prospects

Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von Heijne

1999 • 5,382 citations

Protein Structure Comparison by Alignment of Distance Matrices

1993 • 3,989 citations

Semianalytical treatment of solvation for molecular mechanics and dynamics

1990 • 3,585 citations

Prediction of Protein Secondary Structure at Better than 70% Accuracy

1993 • 2,958 citations

Principles of protein folding — A perspective from simple exact models

1995 • 1,532 citations

Dali: a network tool for protein structure comparison

1995 • 1,447 citations

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions

1997 • 1,403 citations

MIPS: a database for genomes and protein sequences

2000 • 1,295 citations

Unusually stable helix formation in short alanine-based peptides.

1989 • 752 citations

PRINCIPLES THAT DETERMINE THE STRUCTURE OF PROTEINS

1984 • 645 citations

A simple model for calculating the kinetics of protein folding from three-dimensional structures

1999 • 631 citations

Knowledge-based potentials for proteins

1995 • 619 citations

Ab initio protein structure prediction of CASP III targets using ROSETTA

1999 • 542 citations

Atomic solvation parameters applied to molecular dynamics of proteins in solution

1992 • 527 citations

A short linear peptide that folds into a native stable β-hairpin in aqueous solution

1994 • 516 citations

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

1999 • 433 citations

Statistical Potentials Extracted From Protein Structures: How Accurate Are They?

1996 • 428 citations

Energy Functions that Discriminate X-ray and Near-native Folds from Well-constructed Decoys

1996 • 424 citations

Dali/FSSP classification of three-dimensional protein folds

1997 • 423 citations

On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations.

1984 • 386 citations

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

1998 • 358 citations

Prediction of local structure in proteins using a library of sequence-structure motifs

1998 • 346 citations

Additivity Principles in Biochemistry

1997 • 344 citations

A theoretical search for folding/unfolding nuclei in three-dimensional protein structures

1999 • 315 citations

HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins 1 1Edited by J. Thornton

2000 • 309 citations

Monte carlo simulations of protein folding. I. Lattice model and interaction scheme

1994 • 298 citations

Decomposition of the Free Energy of a System in Terms of Specific Interactions

1994 • 292 citations

Structure-derived potentials and protein simulations

1996 • 288 citations

An analysis of incorrectly folded protein models

1984 • 282 citations

LINUS: A hierarchic procedure to predict the fold of a protein

1995 • 270 citations

Discrimination of the native from misfolded protein models with an energy function including implicit solvation

1999 • 269 citations

The complexity and accuracy of discrete state models of protein structure

1995 • 243 citations

Protein folds and functions

1998 • 217 citations

Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to Glutaredoxins/Thioredoxins and T 1 Ribonucleases 1 1Edited by F. Cohen

1998 • 208 citations

De novo protein structure determination using sparse NMR data.

2000 • 182 citations

Ab initio protein structure prediction of CASP III targets using ROSETTA

1999 • 181 citations

Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece

2000 • 179 citations

Critical assessment of methods of protein structure prediction (CASP): Round III

1999 • 173 citations

Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: A prediction of the structure of the catalytic domain of protein kinases

1991 • 173 citations

An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function.

1994 • 172 citations

Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics

1991 • 170 citations

Matching theory and experiment in protein folding

1999 • 164 citations

Factors affecting the ability of energy functions to discriminate correct from incorrect folds

1997 • 164 citations

Exploring conformational space with a simple lattice model for protein structure

1994 • 158 citations

Free energy calculations of ion hydration: an analysis of the Born model in terms of microscopic simulations

1989 • 154 citations

Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin

1994 • 147 citations

CAFASP‐1: Critical assessment of fully automated structure prediction methods

1999 • 144 citations

Potential energy functions for threading

1996 • 143 citations

Ab initio folding of proteins using restraints derived from evolutionary information

1999 • 142 citations

Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins

1982 • 141 citations

Recognizing Native Folds by the Arrangement of Hydrophobic and Polar Residues

1995 • 137 citations

Analysis and assessment of ab initio three‐dimensional prediction, secondary structure, and contacts prediction

1999 • 129 citations

Progress in protein structure prediction

1997 • 128 citations

Predicting protein structure using only sequence information

1999 • 115 citations

An empirical energy potential with a reference state for protein fold and sequence recognition

1999 • 109 citations

Analysis and prediction of protein β-sheet structures by a combinatorial approach

1980 • 105 citations

CAFASP-1: Critical assessment of fully automated structure prediction methods

1999 • 105 citations

Fold and function predictions for Mycoplasma genitalium proteins

1998 • 104 citations

Prediction of loop geometries using a generalized born model of solvation effects

1999 • 104 citations

Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the Glutaredoxin/Thioredoxin disulfide oxidoreductase activity 1 1Edited by F. E. Cohen

1998 • 101 citations

Origins of structural diversity within sequentially identical hexapeptides

1993 • 97 citations

Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments

1998 • 94 citations

Local versus nonlocal interactions in protein folding and stability – an experimentalist's point of view

1996 • 89 citations

Three-dimensional structure analysis of PROSITE patterns 1 1Edited by F. E. Cohen

1999 • 89 citations

Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation

2001 • 88 citations

Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction

1999 • 81 citations

Structure classification-based assessment of CASP3 predictions for the fold recognition targets

1999 • 80 citations

Local sequence-structure correlations in proteins

1996 • 77 citations

Evaluation of current techniques for Ab initio protein structure prediction

1995 • 75 citations

Discrimination of near-native protein structures from misfolded models by empirical free energy functions

2000 • 70 citations

Ab initio protein structure prediction using a combined hierarchical approach

1999 • 70 citations

A COMBINED APPROACH FOR AB INITIO CONSTRUCTION OF LOW RESOLUTION PROTEIN TERTIARY STRUCTURES FROM SEQUENCE

1998 • 67 citations

Strength of Solvent-Exposed Salt-Bridges

1999 • 66 citations

CASP2: Report on ab initio predictions

1997 • 59 citations

Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations

1998 • 56 citations

Ab initio protein structure prediction using a combined hierarchical approach

1999 • 56 citations

DSC: public domain protein secondary structure prediction

1997 • 55 citations

Bona Fide Prediction of Aspects of Protein Conformation

1994 • 53 citations

Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set

1999 • 52 citations

Protein fold irregularities that hinder sequence analysis

1998 • 48 citations

Sustained performance of knowledge-based potentials in fold recognition

1999 • 43 citations

Three‐dimensional structures and contexts associated with recurrent amino acid sequence patterns

1997 • 38 citations

Protein folding from 1961 to 1982.

1999 • 37 citations

Improved recognition of native‐like protein structures using a combination of sequence‐dependent and sequence‐independent features of proteins

1999 • 34 citations

Predicting the structures of 18 peptides using Geocore

1999 • 26 citations

Conformations of peptide fragments from the FK506 binding protein: comparison with the native and urea-unfolded states 1 1Edited by P. E. Wright

1999 • 25 citations

Prediction of protein structure: The problem of fold multiplicity

1999 • 23 citations

Selecting near‐native conformations in homology modeling: The role of molecular mechanics and solvation terms

1998 • 22 citations

Search for the most stable folds of protein chains: II. Computation of stable architectures of β-proteins using a self-consistent molecular field theory

1996 • 17 citations

Structure classification‐based assessment of CASP3 predictions for the fold recognition targets

1999 • 17 citations

Coupling the folding of homologous proteins

1998 • 14 citations

Adjusting potential energy functions for lattice models of chain molecules

1996 • 12 citations

An empirical energy potential with a reference state for protein fold and sequence recognition

1999 • 11 citations

Prediction of protein structure: The problem of fold multiplicity

1999 • 8 citations

Prediction of loop geometries using a generalized born model of solvation effects

1999 • 8 citations

A combinational approach to the prediction of the tertiary fold of globular proteins

1982 • 7 citations

How Homologs Can Help to Predict Protein Folds Even Though They Cannot Be Predicted for Individual Sequences

1998 • 6 citations

Use of MM‐PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece

2000 • 5 citations

Sustained performance of knowledge‐based potentials in fold recognition

1999 • 3 citations

Discrimination of near‐native protein structures from misfolded models by empirical free energy functions

2000 • 2 citations