FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties11Edited by B. Honig

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

1994 • 63,397 citations

The Protein Data Bank

2000 • 35,287 citations

Comparative Protein Modelling by Satisfaction of Spatial Restraints

1993 • 12,640 citations

Improved tools for biological sequence comparison.

1988 • 11,455 citations

A general method applicable to the search for similarities in the amino acid sequence of two proteins

1970 • 11,049 citations

Identification of common molecular subsequences

1981 • 9,753 citations

The protein data bank: A computer-based archival file for macromolecular structures

1977 • 8,627 citations

The rapid generation of mutation data matrices from protein sequences

1992 • 6,766 citations

SCOP: A structural classification of proteins database for the investigation of sequences and structures

1995 • 6,372 citations

Amino acid substitution matrices from protein blocks.

1992 • 5,998 citations

Profile hidden Markov models.

1998 • 5,297 citations

Atlas of protein sequence and structure

1965 • 4,462 citations

The Use of Ranks to Avoid the Assumption of Normality Implicit in the Analysis of Variance

1937 • 4,113 citations

The Use of Ranks to Avoid the Assumption of Normality Implicit in the Analysis of Variance

1937 • 3,577 citations

CATH – a hierarchic classification of protein domain structures

1997 • 2,558 citations

The relation between the divergence of sequence and structure in proteins.

1986 • 2,373 citations

Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins

1974 • 2,173 citations

An improved algorithm for matching biological sequences

1982 • 1,728 citations

Enhanced genome annotation using structural profiles in the program 3D-PSSM 1 1Edited by J. Thornton

2000 • 1,494 citations

Profile analysis: detection of distantly related proteins.

1987 • 1,308 citations

A new approach to protein fold recognition

1992 • 1,239 citations

Hidden Markov models for detecting remote protein homologies.

1998 • 1,122 citations

SCOP: a Structural Classification of Proteins database

1997 • 945 citations

GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences

1999 • 901 citations

Exhaustive Matching of the Entire Protein Sequence Database

1992 • 844 citations

Conformational preferences of amino acids in globular proteins

1978 • 653 citations

Knowledge-based prediction of protein structures and the design of novel molecules

1987 • 653 citations

Knowledge-based potentials for proteins

1995 • 619 citations

Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms

1991 • 582 citations

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods

1998 • 560 citations

Probability Tables for Individual Comparisons by Ranking Methods

1947 • 539 citations

Definition of general topological equivalence in protein structures

1990 • 506 citations

HOMSTRAD: A database of protein structure alignments for homologous families

1998 • 505 citations

[9] Profile analysis

1990 • 486 citations

Comparison of sequence profiles. Strategies for structural predictions using sequence information

2000 • 469 citations

JOY: protein sequence-structure representation and analysis.

1998 • 390 citations

Alternative packing arrangements in the hydrophobic core of λrepresser

1989 • 375 citations

Identification of native protein folds amongst a large number of incorrect models

1990 • 305 citations

Improved sensitivity of profile searches through the use of sequence weights and gap excision

1994 • 301 citations

Protein fold recognition using sequence‐derived predictions

1996 • 299 citations

Analysis of insertions/deletions in protein structures

1992 • 241 citations

Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction

1990 • 215 citations

Protein structure prediction by threading methods: Evaluation of current techniques

1995 • 211 citations

Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling

1987 • 196 citations

Identification of related proteins on family, superfamily and fold level 1 1Edited by F. C. Cohen

2000 • 192 citations

SCOP: a Structural Classification of Proteins database

1999 • 183 citations

Secondary structure‐based profiles: Use of structure‐conserving scoring tables in searching protein sequence databases for structural similarities

1991 • 170 citations

Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions

1995 • 170 citations

Alignment and Searching for Common Protein Folds Using a Data Bank of Structural Templates

1993 • 163 citations

A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence

1997 • 163 citations

Assessing the performance of fold recognition methods by means of a comprehensive benchmark.

1996 • 131 citations

Identification and analysis of domains in proteins

1995 • 125 citations

Alignment of the amino acid sequences of distantly related proteins using variable gap penalties

1986 • 118 citations

Combination of threading potentials and sequence profiles improves fold recognition 1 1Edited by B. Honig

2000 • 116 citations

A fast and sensitive multiple sequence alignment algorithm

1989 • 111 citations

Fragment Ranking in Modelling of Protein Structure

1993 • 110 citations

An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins

1995 • 89 citations

A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%

1995 • 88 citations

Critical evaluation of comparative model building of Streptomyces griseus trypsin

1984 • 83 citations

Weighting in sequence space: a comparison of methods in terms of generalized sequences.

1993 • 82 citations

Hidden Markov models that use predicted secondary structures for fold recognition

1999 • 76 citations

Use of Amino Acid Environment-dependent Substitution Tables and Conformational Propensities in Structure Prediction from Aligned Sequences of Homologous Proteins. II. Secondary Structures

1994 • 63 citations

Comparison of the predicted model of α-lytic protease with the X-ray structure

1979 • 40 citations

An iterative structure‐assisted approach to sequence alignment and comparative modeling

1999 • 32 citations

An iterative structure-assisted approach to sequence alignment and comparative modeling

1999 • 27 citations

Analysis of conservation and substitutions of secondary structure elements within protein superfamilies

2000 • 22 citations

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