Published in Int J Mol Sci on September 10, 2014
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A (1992) 61.33
PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci (1997) 45.07
The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci (1992) 44.38
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene (1988) 42.41
The Ensembl genome database project. Nucleic Acids Res (2002) 40.87
Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol (1978) 29.77
Empirical predictions of protein conformation. Annu Rev Biochem (1978) 25.48
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol (2001) 16.83
The universal protein resource (UniProt). Nucleic Acids Res (2007) 16.33
Amino acid difference formula to help explain protein evolution. Science (1974) 15.19
The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32
Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry (1974) 12.07
WoLF PSORT: protein localization predictor. Nucleic Acids Res (2007) 10.14
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci U S A (2004) 7.42
The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci U S A (1984) 6.36
Mutagenic deamination of cytosine residues in DNA. Nature (1980) 6.26
Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins (2000) 6.22
Two types of amino acid substitutions in protein evolution. J Mol Evol (1979) 4.34
Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci (1994) 3.94
An analysis of protein domain linkers: their classification and role in protein folding. Protein Eng (2002) 2.69
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res (2012) 2.68
Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci (1992) 2.61
Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci (1990) 2.53
Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome. Genome Res (2002) 2.49
Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol (2003) 2.16
DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics (2012) 2.14
Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics (1998) 2.05
The influence of nearest neighbors on the rate and pattern of spontaneous point mutations. J Mol Evol (1992) 1.96
Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins (1991) 1.88
An analysis of side chain interactions and pair correlations within antiparallel beta-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs. Proteins (1995) 1.87
Combining protein evolution and secondary structure. Mol Biol Evol (1996) 1.81
Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables. J Mol Biol (1993) 1.60
Determinants of strand register in antiparallel beta-sheets of proteins. Protein Sci (1998) 1.55
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Relationship between the occurrence of cysteine in proteins and the complexity of organisms. Mol Biol Evol (2000) 1.53
Assessing site-interdependent phylogenetic models of sequence evolution. Mol Biol Evol (2006) 1.42
Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic Acids Res (2012) 1.38
Amino acid repeat patterns in protein sequences: their diversity and structural-functional implications. Protein Sci (2000) 1.36
Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene (2005) 1.30
Helix-stabilizing interaction between tyrosine and leucine or valine when the spacing is i, i + 4. J Mol Biol (1994) 1.29
Amino acid pairing preferences in parallel beta-sheets in proteins. J Mol Biol (2005) 1.17
Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats. Genomics (2006) 1.09
Exploring the sequence patterns in the alpha-helices of proteins. Protein Eng (2003) 1.05
Biophysical and structural considerations for protein sequence evolution. BMC Evol Biol (2011) 1.04
Genome-wide evidence for selection acting on single amino acid repeats. Genome Res (2010) 1.00
On the significance of alternating patterns of polar and non-polar residues in beta-strands. J Mol Biol (2002) 0.99
Sequence codes for extended conformation: a neighbor-dependent sequence analysis of loops in proteins. Proteins (2001) 0.98
Tests for helix-stabilizing interactions between various nonpolar side chains in alanine-based peptides. Protein Sci (1994) 0.97
Statistical potentials for improved structurally constrained evolutionary models. Mol Biol Evol (2010) 0.96
Role of low-complexity sequences in the formation of novel protein coding sequences. Mol Biol Evol (2011) 0.92
Context dependent substitution biases vary within the human genome. BMC Bioinformatics (2010) 0.90
Evaluation of the effect of CpG hypermutability on human codon substitution. Gene (2008) 0.89
Stabilizing nonpolar/polar side-chain interactions in the alpha-helix. Proteins (2001) 0.87
New words in human mutagenesis. BMC Bioinformatics (2011) 0.87
Amino acid pairing at the N- and C-termini of helical segments in proteins. Proteins (2008) 0.85
Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences. BMC Evol Biol (2010) 0.85
Evaluation of models for the evolution of protein sequences and functions under structural constraint. Biophys Chem (2006) 0.84
Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. J Mol Evol (2010) 0.83
Local-scale repetitiveness in amino acid use in eukaryote protein sequences: a genomic factor in protein evolution. Proteins (1999) 0.83
Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer. Proteins (2012) 0.82
Patterns of nucleotides that flank substitutions in human orthologous genes. BMC Genomics (2010) 0.80
Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins. J Theor Biol (2010) 0.80
Neighboring-site effects of amino acid mutation. Biochem Biophys Res Commun (2006) 0.77
Nearest-neighbor effects and structural preferences in dipeptides are a function of the electronic properties of amino acid side-chains. Proteins (2006) 0.76