Published in BMC Bioinformatics on January 25, 2008
Characterization and prediction of residues determining protein functional specificity. Bioinformatics (2008) 1.80
Exploring the structure and function paradigm. Curr Opin Struct Biol (2008) 1.26
Conserved residue clusters at protein-protein interfaces and their use in binding site identification. BMC Bioinformatics (2010) 1.14
Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification. PLoS Comput Biol (2010) 1.07
Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics (2009) 0.98
Comparing the functional roles of nonconserved sequence positions in homologous transcription repressors: implications for sequence/function analyses. J Mol Biol (2009) 0.88
A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information. BMC Bioinformatics (2011) 0.88
Functionally important positions can comprise the majority of a protein's architecture. Proteins (2011) 0.87
SitesIdentify: a protein functional site prediction tool. BMC Bioinformatics (2009) 0.87
Computational analysis of C-reactive protein for assessment of molecular dynamics and interaction properties. Cell Biochem Biophys (2013) 0.76
Comparison of different ranking methods in protein-ligand binding site prediction. Int J Mol Sci (2012) 0.76
Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. BMC Bioinformatics (2015) 0.75
Dynamic Roles for the N-terminus of the Yeast G Protein-Coupled Receptor Ste2p. Biochim Biophys Acta (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res (1997) 175.36
The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol (1977) 90.57
The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology (1982) 79.76
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins (1991) 32.50
A method of comparing the areas under receiver operating characteristic curves derived from the same cases. Radiology (1983) 30.77
CATH--a hierarchic classification of protein domain structures. Structure (1997) 29.95
Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins (1997) 26.91
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res (2005) 10.60
Note on the sampling error of the difference between correlated proportions or percentages. Psychometrika (1947) 10.31
An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J Exp Med (1970) 9.83
Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J Mol Biol (1987) 9.74
Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci (1993) 9.38
An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol (1996) 9.31
PQS: a protein quaternary structure file server. Trends Biochem Sci (1998) 9.24
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res (2003) 7.79
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76
Scoring residue conservation. Proteins (2002) 4.66
Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics (2002) 4.54
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol (2004) 3.62
Predicting functionally important residues from sequence conservation. Bioinformatics (2007) 3.42
Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng (2001) 3.36
A method to predict functional residues in proteins. Nat Struct Biol (1995) 3.33
Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol (1999) 3.22
ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol (2001) 3.14
The classification of amino acid conservation. J Theor Biol (1986) 3.12
Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins (2001) 3.00
Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics (2004) 2.93
An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol (2003) 2.87
Automatic methods for predicting functionally important residues. J Mol Biol (2003) 2.39
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol (2001) 2.17
Average core structures and variability measures for protein families: application to the immunoglobulins. J Mol Biol (1995) 1.66
SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res (2004) 1.57
Bayesian search of functionally divergent protein subgroups and their function specific residues. Bioinformatics (2006) 1.51
Evolutionary conservation of RecA genes in relation to protein structure and function. J Bacteriol (1996) 1.49
Accurate and scalable identification of functional sites by evolutionary tracing. J Struct Funct Genomics (2003) 1.44
Resolution of hypervariable regions in T-cell receptor beta chains by a modified Wu-Kabat index of amino acid diversity. Proc Natl Acad Sci U S A (1990) 1.36
The variable and conserved interfaces of modeled olfactory receptor proteins. Protein Sci (1999) 1.34
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. Nucleic Acids Res (2007) 1.15
Three-dimensional structure of 2-amino-3-ketobutyrate CoA ligase from Escherichia coli complexed with a PLP-substrate intermediate: inferred reaction mechanism. Biochemistry (2001) 1.13
Computational approaches to gene prediction. J Microbiol (2006) 1.06
Predicting functional sites with an automated algorithm suitable for heterogeneous datasets. BMC Bioinformatics (2005) 0.97
Crystal structure of Trypanosoma cruzi tyrosine aminotransferase: substrate specificity is influenced by cofactor binding mode. Protein Sci (1999) 0.94
Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters. J Theor Biol (1995) 0.93
MINER: software for phylogenetic motif identification. Nucleic Acids Res (2005) 0.92
Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) 31.84
The Jalview Java alignment editor. Bioinformatics (2004) 21.74
The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res (2006) 4.64
Emerging roles of pseudokinases. Trends Cell Biol (2006) 4.48
OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics (2003) 4.01
Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA (2009) 3.87
System-wide changes to SUMO modifications in response to heat shock. Sci Signal (2009) 3.50
A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science (2011) 2.50
MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics (2006) 2.23
Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput Biol (2009) 2.06
Regulation of the miR-212/132 locus by MSK1 and CREB in response to neurotrophins. Biochem J (2010) 1.94
PIPs: human protein-protein interaction prediction database. Nucleic Acids Res (2008) 1.91
TarO: a target optimisation system for structural biology. Nucleic Acids Res (2008) 1.89
The Scottish Structural Proteomics Facility: targets, methods and outputs. J Struct Funct Genomics (2010) 1.66
Classification and functional annotation of eukaryotic protein kinases. Proteins (2007) 1.62
Characterization and prediction of protein nucleolar localization sequences. Nucleic Acids Res (2010) 1.40
The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol (2007) 1.38
Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res (2011) 1.35
Visualization of multiple alignments, phylogenies and gene family evolution. Nat Methods (2010) 1.34
Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation. Nat Struct Mol Biol (2012) 1.34
Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases. EMBO J (2009) 1.32
Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics (2007) 1.31
Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects. J Allergy Clin Immunol (2013) 1.30
Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation. Proc Natl Acad Sci U S A (2012) 1.29
PTEN protein phosphatase activity correlates with control of gene expression and invasion, a tumor-suppressing phenotype, but not with AKT activity. Sci Signal (2012) 1.15
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. Nucleic Acids Res (2007) 1.15
A normalised scale for structural genomics target ranking: the OB-Score. FEBS Lett (2006) 1.15
Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res (2008) 1.12
The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4. EMBO J (2011) 1.11
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. Bioinformatics (2008) 1.10
Haploinsufficiency for AAGAB causes clinically heterogeneous forms of punctate palmoplantar keratoderma. Nat Genet (2012) 1.08
NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. BMC Bioinformatics (2011) 1.06
The complement of protein kinases of the microsporidium Encephalitozoon cuniculi in relation to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe. BMC Genomics (2007) 1.04
Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Res (2011) 1.04
Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA. Bioinformatics (2011) 1.00
A new family of transcription factors. Development (2008) 0.98
Identification of a glycosylphosphatidylinositol anchor-modifying beta1-3 N-acetylglucosaminyl transferase in Trypanosoma brucei. Mol Microbiol (2008) 0.96
The kinomes of apicomplexan parasites. Microbes Infect (2012) 0.96
Quantification of the variation in percentage identity for protein sequence alignments. BMC Bioinformatics (2006) 0.94
Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. Mol Biol Cell (2010) 0.94
PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities. BMC Res Notes (2011) 0.92
Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA. PLoS Genet (2013) 0.91
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus. BMC Syst Biol (2011) 0.89
Biological units and their effect upon the properties and prediction of protein-protein interactions. J Mol Biol (2006) 0.89
Genome analysis of the unicellular green alga Chlamydomonas reinhardtii Indicates an ancient evolutionary origin for key pattern recognition and cell-signaling protein families. Genetics (2008) 0.88
Increased coverage obtained by combination of methods for protein sequence database searching. Bioinformatics (2003) 0.88
A comparison of SCOP and CATH with respect to domain-domain interactions. Proteins (2008) 0.85
XANNpred: neural nets that predict the propensity of a protein to yield diffraction-quality crystals. Proteins (2011) 0.85
The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation. Sci Rep (2013) 0.83
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. Nucleic Acids Res (2008) 0.82
Purification, crystallization and data collection of methicillin-resistant Staphylococcus aureus Sar2676, a pantothenate synthetase. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 0.81
Expression, purification, crystallization, data collection and preliminary biochemical characterization of methicillin-resistant Staphylococcus aureus Sar2028, an aspartate/tyrosine/phenylalanine pyridoxal-5'-phosphate-dependent aminotransferase. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 0.81
Elevated O-GlcNAc levels activate epigenetically repressed genes and delay mouse ESC differentiation without affecting naïve to primed cell transition. Stem Cells (2014) 0.80
Computational approaches to selecting and optimising targets for structural biology. Methods (2011) 0.77
Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA (2016) 0.76
PNAC: a protein nucleolar association classifier. BMC Genomics (2011) 0.76
Visual representation of database search results: the RHIMS Plot. Bioinformatics (2003) 0.75