Published in J Mol Biol on March 05, 2004
Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res (2011) 10.99
Identification of a candidate therapeutic autophagy-inducing peptide. Nature (2013) 3.76
Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol (2007) 3.46
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol (2009) 2.82
Emerging methods in protein co-evolution. Nat Rev Genet (2013) 2.72
Supergenomic network compression and the discovery of EXP1 as a glutathione transferase inhibited by artesunate. Cell (2014) 1.91
Characterization and prediction of residues determining protein functional specificity. Bioinformatics (2008) 1.80
INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification. Bioinformatics (2008) 1.42
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics (2008) 1.41
Sequence comparison by sequence harmony identifies subtype-specific functional sites. Nucleic Acids Res (2006) 1.40
Sequence variation in ligand binding sites in proteins. BMC Bioinformatics (2005) 1.37
Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors. Proc Natl Acad Sci U S A (2010) 1.32
Predicting specificity-determining residues in two large eukaryotic transcription factor families. Nucleic Acids Res (2005) 1.30
PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic Acids Res (2008) 1.30
Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures. BMC Bioinformatics (2012) 1.29
Effective function annotation through catalytic residue conservation. Proc Natl Acad Sci U S A (2005) 1.28
Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics (2006) 1.27
Exploring the structure and function paradigm. Curr Opin Struct Biol (2008) 1.26
De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS One (2008) 1.20
Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information. PLoS Comput Biol (2008) 1.19
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res (2016) 1.18
Membrane protein prediction methods. Methods (2007) 1.17
Evolutionary trace annotation of protein function in the structural proteome. J Mol Biol (2009) 1.16
An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. Algorithms Mol Biol (2010) 1.11
Active site prediction using evolutionary and structural information. Bioinformatics (2010) 1.09
A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness. Genome Res (2014) 1.08
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis. Nucleic Acids Res (2009) 1.08
Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity. Protein Sci (2006) 1.08
Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset. PLoS Comput Biol (2013) 1.07
Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling. PLoS Comput Biol (2009) 1.07
Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites. PLoS Genet (2011) 1.07
Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification. PLoS Comput Biol (2010) 1.07
Dual regulation of cytosolic ascorbate peroxidase (APX) by tyrosine nitration and S-nitrosylation. J Exp Bot (2013) 1.06
Evolutionary Action Score of TP53 Identifies High-Risk Mutations Associated with Decreased Survival and Increased Distant Metastases in Head and Neck Cancer. Cancer Res (2015) 1.05
Role for the regulator of G-protein signaling homology domain of G protein-coupled receptor kinases 5 and 6 in beta 2-adrenergic receptor and rhodopsin phosphorylation. Mol Pharmacol (2009) 1.05
TreeDet: a web server to explore sequence space. Nucleic Acids Res (2006) 1.05
Identification of the ligand binding sites on the molecular surface of proteins. Protein Sci (2005) 1.04
Molecular defects in human carbamoy phosphate synthetase I: mutational spectrum, diagnostic and protein structure considerations. Hum Mutat (2011) 1.04
Functional rescue of beta-adrenoceptor dimerization and trafficking by pharmacological chaperones. Traffic (2009) 1.03
Analysis of the plasticity of location of the Arg244 positive charge within the active site of the TEM-1 beta-lactamase. Protein Sci (2009) 1.03
A comparative structural bioinformatics analysis of the insulin receptor family ectodomain based on phylogenetic information. PLoS One (2008) 1.02
Quality assessment of protein model-structures using evolutionary conservation. Bioinformatics (2010) 1.01
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. Bioinformatics (2009) 1.00
Protein function prediction: towards integration of similarity metrics. Curr Opin Struct Biol (2011) 1.00
Evolution: a guide to perturb protein function and networks. Curr Opin Struct Biol (2010) 0.97
Single nucleotide variations: biological impact and theoretical interpretation. Protein Sci (2014) 0.97
Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities. PLoS One (2010) 0.96
Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation. Protein Sci (2010) 0.96
Local packing density is the main structural determinant of the rate of protein sequence evolution at site level. Biomed Res Int (2014) 0.94
Evolutionary trace for prediction and redesign of protein functional sites. Methods Mol Biol (2012) 0.94
Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives. Proteins (2008) 0.93
Structural requirements for interaction of peroxisomal targeting signal 2 and its receptor PEX7. J Biol Chem (2011) 0.93
Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms. Stat Appl Genet Mol Biol (2011) 0.93
Accounting for epistatic interactions improves the functional analysis of protein structures. Bioinformatics (2013) 0.92
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev (2016) 0.92
A comparative study of conservation and variation scores. BMC Bioinformatics (2010) 0.91
Conservation analysis of the CydX protein yields insights into small protein identification and evolution. BMC Genomics (2014) 0.90
Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. Protein Sci (2005) 0.90
Solution structure of inhibitor-free human metalloelastase (MMP-12) indicates an internal conformational adjustment. J Mol Biol (2007) 0.89
A combinatorial approach to detect coevolved amino acid networks in protein families of variable divergence. PLoS Comput Biol (2009) 0.88
A conserved motif flags acyl carrier proteins for β-branching in polyketide synthesis. Nat Chem Biol (2013) 0.88
Differential effects of collagen prolyl 3-hydroxylation on skeletal tissues. PLoS Genet (2014) 0.87
Prediction and experimental validation of enzyme substrate specificity in protein structures. Proc Natl Acad Sci U S A (2013) 0.87
ResBoost: characterizing and predicting catalytic residues in enzymes. BMC Bioinformatics (2009) 0.87
Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction. BMC Bioinformatics (2012) 0.86
Binding interface prediction by combining protein-protein docking results. Proteins (2013) 0.86
Regulation of Ras localization and cell transformation by evolutionarily conserved palmitoyltransferases. Mol Cell Biol (2013) 0.84
Selectivity and evolutionary divergence of metabotropic glutamate receptors for endogenous ligands and G proteins coupled to phospholipase C or TRP channels. J Biol Chem (2014) 0.82
Determinants, discriminants, conserved residues--a heuristic approach to detection of functional divergence in protein families. PLoS One (2011) 0.82
Protein fragments: functional and structural roles of their coevolution networks. PLoS One (2012) 0.82
Determinants of endogenous ligand specificity divergence among metabotropic glutamate receptors. J Biol Chem (2014) 0.82
The dimeric SOS mutagenesis protein UmuD is active as a monomer. J Biol Chem (2010) 0.82
It's more than stamp collecting: how genome sequencing can unify biological research. Trends Genet (2015) 0.82
Sequence, structure and ligand binding evolution of rhodopsin-like G protein-coupled receptors: a crystal structure-based phylogenetic analysis. PLoS One (2015) 0.81
Algorithmic approaches to protein-protein interaction site prediction. Algorithms Mol Biol (2015) 0.81
Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions. PLoS Comput Biol (2015) 0.81
Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases. Biol Direct (2010) 0.81
WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families. Nucleic Acids Res (2005) 0.81
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes. PLoS Biol (2016) 0.80
Differential molecular response of monodehydroascorbate reductase and glutathione reductase by nitration and S-nitrosylation. J Exp Bot (2015) 0.80
Structure-based Methods for Computational Protein Functional Site Prediction. Comput Struct Biotechnol J (2013) 0.80
Function prediction from networks of local evolutionary similarity in protein structure. BMC Bioinformatics (2013) 0.80
Prediction and redesign of protein-protein interactions. Prog Biophys Mol Biol (2014) 0.80
Identification of functionally important residues/domains in membrane proteins using an evolutionary approach coupled with systematic mutational analysis. Methods Mol Biol (2009) 0.80
Recent advances in functional region prediction by using structural and evolutionary information - Remaining problems and future extensions. Comput Struct Biotechnol J (2013) 0.80
ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape. Bioinformatics (2012) 0.79
Functional region prediction with a set of appropriate homologous sequences--an index for sequence selection by integrating structure and sequence information with spatial statistics. BMC Struct Biol (2012) 0.79
Negative feedback in genetic circuits confers evolutionary resilience and capacitance. Cell Rep (2014) 0.79
Background frequencies for residue variability estimates: BLOSUM revisited. BMC Bioinformatics (2007) 0.79
Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores. Proteins (2015) 0.78
LigProf: a simple tool for in silico prediction of ligand-binding sites. J Mol Model (2007) 0.78
A protein sequence meta-functional signature for calcium binding residue prediction. Pattern Recognit Lett (2010) 0.78
L1pred: a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier. PLoS One (2012) 0.78
Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction. Adv Appl Bioinform Chem (2009) 0.77
The Thr-His Connection on the Distal Heme of Catalase-Related Hemoproteins: A Hallmark of Reaction with Fatty Acid Hydroperoxides. Chembiochem (2016) 0.77
A conservation and biophysics guided stochastic approach to refining docked multimeric proteins. BMC Struct Biol (2013) 0.77
Lessons in Protein Design from Combined Evolution and Conformational Dynamics. Sci Rep (2015) 0.77
Protein-protein interface detection using the energy centrality relationship (ECR) characteristic of proteins. PLoS One (2014) 0.77
Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations. PLoS Comput Biol (2016) 0.75
Codon-level co-occurrences of germline variants and somatic mutations in cancer are rare but often lead to incorrect variant annotation and underestimated impact prediction. PLoS One (2017) 0.75
Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F. Nature (1996) 2.55
Influence of mutation type and X chromosome inactivation on Rett syndrome phenotypes. Ann Neurol (2000) 2.03
Receptor and betagamma binding sites in the alpha subunit of the retinal G protein transducin. Science (1997) 1.71
Prediction and confirmation of a site critical for effector regulation of RGS domain activity. Nat Struct Biol (2001) 1.42
An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics (2005) 1.38
Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996. Fold Des (1997) 1.36
Similar structures and shared switch mechanisms of the beta2-adrenoceptor and the parathyroid hormone receptor. Zn(II) bridges between helices III and VI block activation. J Biol Chem (1999) 1.36
A genome-wide search for synaptic vesicle cycle proteins in Drosophila. Neuron (2000) 1.32
Evolutionary trace report_maker: a new type of service for comparative analysis of proteins. Bioinformatics (2006) 1.30
Some model experiments in hemodynamics: VI. Two-body collisions between blood cells. Biorheology (1981) 1.24
A regulator of G protein signaling interaction surface linked to effector specificity. Proc Natl Acad Sci U S A (2000) 1.15
C5a receptor activation. Genetic identification of critical residues in four transmembrane helices. J Biol Chem (1999) 1.10
Combining inference from evolution and geometric probability in protein structure evaluation. J Mol Biol (2003) 1.10
Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation. Protein Sci (2010) 0.96
The murine Polycomb-group gene eed and its human orthologue: functional implications of evolutionary conservation. Genomics (1998) 0.96
Genetic mapping of the human C5a receptor. Identification of transmembrane amino acids critical for receptor function. J Biol Chem (2000) 0.90
Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins. Proteins (2006) 0.89
A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins. Bioinformatics (2005) 0.87
Getting past appearances: the many-fold consequences of remote homology. Nat Struct Biol (2001) 0.83
On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues. J Mol Biol (2007) 0.81
Background frequencies for residue variability estimates: BLOSUM revisited. BMC Bioinformatics (2007) 0.79
The structure of proteins and their binding sites: NMR and artificial intelligence. Prog Clin Biol Res (1989) 0.75