Published in Bioinformatics on February 08, 2005
CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics (2006) 4.11
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol (2006) 3.54
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics (2009) 3.00
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol (2009) 2.82
Fpocket: an open source platform for ligand pocket detection. BMC Bioinformatics (2009) 2.42
3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Res (2010) 2.20
PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem Cent J (2007) 1.90
Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res (2009) 1.85
SITEHOUND-web: a server for ligand binding site identification in protein structures. Nucleic Acids Res (2009) 1.82
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics (2010) 1.72
A different function for a member of an ancient and highly conserved cytochrome P450 family: from essential sterols to plant defense. Proc Natl Acad Sci U S A (2006) 1.71
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics (2007) 1.70
LigASite--a database of biologically relevant binding sites in proteins with known apo-structures. Nucleic Acids Res (2007) 1.53
Computational methods in drug discovery. Pharmacol Rev (2013) 1.51
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47
Minimal pharmacophoric elements and fragment hopping, an approach directed at molecular diversity and isozyme selectivity. Design of selective neuronal nitric oxide synthase inhibitors. J Am Chem Soc (2008) 1.47
The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput Biol (2008) 1.44
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement. Structure (2012) 1.42
INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification. Bioinformatics (2008) 1.42
fpocket: online tools for protein ensemble pocket detection and tracking. Nucleic Acids Res (2010) 1.40
PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. PLoS Comput Biol (2009) 1.35
MolAxis: efficient and accurate identification of channels in macromolecules. Proteins (2008) 1.30
Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS One (2010) 1.29
The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. Nat Protoc (2015) 1.26
2P2Idb: a structural database dedicated to orthosteric modulation of protein-protein interactions. Nucleic Acids Res (2012) 1.25
FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics (2011) 1.25
Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach. Chem Biol Drug Des (2010) 1.24
Binding ligand prediction for proteins using partial matching of local surface patches. Int J Mol Sci (2010) 1.23
PocketMatch: a new algorithm to compare binding sites in protein structures. BMC Bioinformatics (2008) 1.23
Pharmacological chaperones stabilize retromer to limit APP processing. Nat Chem Biol (2014) 1.21
Functional analysis of free methionine-R-sulfoxide reductase from Saccharomyces cerevisiae. J Biol Chem (2008) 1.19
Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites. Proteins (2009) 1.17
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Res (2011) 1.16
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. BMC Bioinformatics (2010) 1.15
Selective prediction of interaction sites in protein structures with THEMATICS. BMC Bioinformatics (2007) 1.14
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Res (2011) 1.12
Real-time ligand binding pocket database search using local surface descriptors. Proteins (2010) 1.12
FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins. BMC Bioinformatics (2011) 1.11
MolAxis: a server for identification of channels in macromolecules. Nucleic Acids Res (2008) 1.10
Active site prediction using evolutionary and structural information. Bioinformatics (2010) 1.09
Using a fragment-based approach to target protein-protein interactions. Chembiochem (2013) 1.09
Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors. PLoS One (2007) 1.09
Comparative surface geometry of the protein kinase family. Protein Sci (2009) 1.08
Prediction of functional sites based on the fuzzy oil drop model. PLoS Comput Biol (2007) 1.08
MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. BMC Bioinformatics (2008) 1.07
Fast dynamics perturbation analysis for prediction of protein functional sites. BMC Struct Biol (2008) 1.06
EasyMIFS and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures. Bioinformatics (2009) 1.06
Evaluation of SSYA10-001 as a replication inhibitor of severe acute respiratory syndrome, mouse hepatitis, and Middle East respiratory syndrome coronaviruses. Antimicrob Agents Chemother (2014) 1.04
Four-alpha-helix bundle with designed anesthetic binding pockets. Part II: halothane effects on structure and dynamics. Biophys J (2008) 1.03
SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns. Nucleic Acids Res (2009) 1.03
McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm. J Mol Model (2009) 1.02
A novel and efficient tool for locating and characterizing protein cavities and binding sites. Proteins (2010) 1.01
Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins. Nucleic Acids Res (2013) 1.01
Chitohexaose activates macrophages by alternate pathway through TLR4 and blocks endotoxemia. PLoS Pathog (2012) 1.00
Multi-species analyses of direct activators of the constitutive androstane receptor. Toxicol Sci (2011) 1.00
Efficacy of E. officinalis on the cariogenic properties of Streptococcus mutans: a novel and alternative approach to suppress quorum-sensing mechanism. PLoS One (2012) 1.00
The influenza virus NS1 protein as a therapeutic target. Antiviral Res (2013) 0.99
A position-specific distance-dependent statistical potential for protein structure and functional study. Structure (2012) 0.99
Lessons for fragment library design: analysis of output from multiple screening campaigns. J Comput Aided Mol Des (2009) 0.98
Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface. PLoS Comput Biol (2013) 0.98
Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics (2009) 0.98
Assessment for the identification of better HDAC inhibitor class through binding energy calculations and descriptor analysis. Bioinformation (2008) 0.97
What induces pocket openings on protein surface patches involved in protein-protein interactions? J Comput Aided Mol Des (2008) 0.97
Selective phthalate activation of naturally occurring human constitutive androstane receptor splice variants and the pregnane X receptor. Toxicol Sci (2011) 0.97
Predicting small ligand binding sites in proteins using backbone structure. Bioinformatics (2008) 0.97
Activation of p115-RhoGEF requires direct association of Gα13 and the Dbl homology domain. J Biol Chem (2012) 0.97
Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet (Setaria italica L.). PLoS One (2014) 0.96
Design of protein membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V. Proc Natl Acad Sci U S A (2007) 0.96
Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins. BMC Bioinformatics (2007) 0.96
Insights from modeling the 3D structure of New Delhi metallo-β-lactamse and its binding interactions with antibiotic drugs. PLoS One (2011) 0.95
Predicting gene ontology functions from protein's regional surface structures. BMC Bioinformatics (2007) 0.95
KVFinder: steered identification of protein cavities as a PyMOL plugin. BMC Bioinformatics (2014) 0.95
Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures. J Struct Funct Genomics (2011) 0.94
Linking genotype and phenotype of Saccharomyces cerevisiae strains reveals metabolic engineering targets and leads to triterpene hyper-producers. PLoS One (2011) 0.94
Where does amantadine bind to the influenza virus M2 proton channel? Trends Biochem Sci (2010) 0.94
The maize ALDH protein superfamily: linking structural features to functional specificities. BMC Struct Biol (2010) 0.94
Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics (2009) 0.94
A structure-based approach for detection of thiol oxidoreductases and their catalytic redox-active cysteine residues. PLoS Comput Biol (2009) 0.93
Insights into the mutation-induced HHH syndrome from modeling human mitochondrial ornithine transporter-1. PLoS One (2012) 0.93
Assessment of ligand binding site predictions in CASP10. Proteins (2014) 0.93
Binding-site assessment by virtual fragment screening. PLoS One (2010) 0.93
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev (2016) 0.92
Ligand-binding site prediction of proteins based on known fragment-fragment interactions. Bioinformatics (2010) 0.91
Predicting nonspecific ion binding using DelPhi. Biophys J (2012) 0.91
Flexibility and small pockets at protein-protein interfaces: New insights into druggability. Prog Biophys Mol Biol (2015) 0.90
Casein fermentate of Lactobacillus animalis DPC6134 contains a range of novel propeptide angiotensin-converting enzyme inhibitors. Appl Environ Microbiol (2007) 0.90
Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines. Protein Sci (2007) 0.90
Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase. PLoS One (2011) 0.90
A strategy based on protein-protein interface motifs may help in identifying drug off-targets. J Chem Inf Model (2012) 0.90
Inhibitory effect of zingiber officinale towards Streptococcus mutans virulence and caries development: in vitro and in vivo studies. BMC Microbiol (2015) 0.89
HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information. BMC Bioinformatics (2011) 0.89
Redox biology: computational approaches to the investigation of functional cysteine residues. Antioxid Redox Signal (2011) 0.89
Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction. J Comput Aided Mol Des (2010) 0.88
Insight to pyrazinamide resistance in Mycobacterium tuberculosis by molecular docking. Bioinformation (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
SitesIdentify: a protein functional site prediction tool. BMC Bioinformatics (2009) 0.87
Knowledge-based annotation of small molecule binding sites in proteins. BMC Bioinformatics (2010) 0.87
Investigating the structure and dynamics of the PIK3CA wild-type and H1047R oncogenic mutant. PLoS Comput Biol (2014) 0.86
Computational structural and functional analysis of hypothetical proteins of Staphylococcus aureus. Bioinformation (2012) 0.86
Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. J R Soc Interface (2011) 0.86
Mutations involved in Aicardi-Goutières syndrome implicate SAMHD1 as regulator of the innate immune response. Nat Genet (2009) 5.84
Mutations in LRP5 or FZD4 underlie the common familial exudative vitreoretinopathy locus on chromosome 11q. Am J Hum Genet (2004) 2.70
The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol (2010) 2.07
Ligand binding: functional site location, similarity and docking. Curr Opin Struct Biol (2003) 1.78
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic Acids Res (2006) 1.62
SitesBase: a database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res (2006) 1.61
Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces. Bioinformatics (2006) 1.58
An evaluation of automated homology modelling methods at low target template sequence similarity. Bioinformatics (2007) 1.57
Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. J Mol Biol (2005) 1.46
Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships. Bioinformatics (2005) 1.45
Predicting druggable binding sites at the protein-protein interface. Drug Discov Today (2008) 1.45
Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sci (2006) 1.36
Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching. Proteins (2004) 1.34
Further studies on hepatitis C virus NS5A-SH3 domain interactions: identification of residues critical for binding and implications for viral RNA replication and modulation of cell signalling. J Gen Virol (2005) 1.04
Binding site similarity analysis for the functional classification of the protein kinase family. J Chem Inf Model (2009) 1.04
Angiotensin-converting enzyme-2 (ACE2): comparative modeling of the active site, specificity requirements, and chloride dependence. Biochemistry (2003) 1.04
A machine learning-based method to improve docking scoring functions and its application to drug repurposing. J Chem Inf Model (2011) 1.03
Delineation and modelling of a nucleolar retention signal in the coronavirus nucleocapsid protein. Traffic (2006) 0.96
InCa-SiteFinder: a method for structure-based prediction of inositol and carbohydrate binding sites on proteins. J Mol Graph Model (2009) 0.94
ReverseScreen3D: a structure-based ligand matching method to identify protein targets. J Chem Inf Model (2011) 0.90
Hierarchical bayesian modeling of pharmacophores in bioinformatics. Biometrics (2010) 0.89
BAYESIAN ALIGNMENT OF SIMILARITY SHAPES. Ann Appl Stat (2013) 0.86
A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. J Chem Inf Model (2006) 0.86
Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE. BMC Genomics (2007) 0.84
Structure-based pharmacophore design and virtual screening for novel angiotensin converting enzyme 2 inhibitors. J Chem Inf Model (2006) 0.84
Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking. Bioinformatics (2007) 0.83
LigMatch: a multiple structure-based ligand matching method for 3D virtual screening. J Chem Inf Model (2009) 0.83
Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable. PLoS One (2012) 0.83
Identification of critical active-site residues in angiotensin-converting enzyme-2 (ACE2) by site-directed mutagenesis. FEBS J (2005) 0.83
Comparison of the ATP binding sites of protein kinases using conformationally diverse bisindolylmaleimides. J Am Chem Soc (2005) 0.81
Homology-modelling protein-ligand interactions: allowing for ligand-induced conformational change. J Mol Biol (2010) 0.79
Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities. J Phys Chem B (2012) 0.78
Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity. J Chem Inf Model (2008) 0.78
Correction to "Machine learning-based method to improve docking scoring functions and its application to drug repurposing". J Chem Inf Model (2011) 0.75
Toward the discovery of functional transthyretin amyloid inhibitors: application of virtual screening methods. J Chem Inf Model (2010) 0.75