Recognition of functional sites in protein structures.

Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLoS Comput Biol (2009) 2.84

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A (2008) 2.44

Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A (2004) 1.96

Chemogenomic approaches to rational drug design. Br J Pharmacol (2007) 1.74

SitesBase: a database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res (2006) 1.61

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res (2008) 1.52

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics (2009) 1.46

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics (2008) 1.41

Comparative analysis of protein structure alignments. BMC Struct Biol (2007) 1.28

Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol (2007) 1.22

De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS One (2008) 1.20

SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res (2005) 1.20

APoc: large-scale identification of similar protein pockets. Bioinformatics (2013) 1.18

Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties. PLoS Comput Biol (2009) 1.17

Evolutionary trace annotation of protein function in the structural proteome. J Mol Biol (2009) 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

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity. Protein Sci (2006) 1.08

Fast dynamics perturbation analysis for prediction of protein functional sites. BMC Struct Biol (2008) 1.06

Fast screening of protein surfaces using geometric invariant fingerprints. Proc Natl Acad Sci U S A (2009) 1.05

Prediction of interacting single-stranded RNA bases by protein-binding patterns. J Mol Biol (2008) 1.04

Identification of the ligand binding sites on the molecular surface of proteins. Protein Sci (2005) 1.04

A comprehensive survey of small-molecule binding pockets in proteins. PLoS Comput Biol (2013) 1.04

Relating destabilizing regions to known functional sites in proteins. BMC Bioinformatics (2007) 1.02

SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Res (2010) 1.00

Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding. PLoS Comput Biol (2011) 1.00

Structure-based in silico identification of ubiquitin-binding domains provides insights into the ALIX-V:ubiquitin complex and retrovirus budding. EMBO J (2013) 0.98

BioInfo3D: a suite of tools for structural bioinformatics. Nucleic Acids Res (2004) 0.97

BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement. J Struct Biol (2011) 0.95

The LabelHash algorithm for substructure matching. BMC Bioinformatics (2010) 0.94

Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics (2009) 0.94

Superpose3D: a local structural comparison program that allows for user-defined structure representations. PLoS One (2010) 0.94

Rapid comparison of protein binding site surfaces with property encoded shape distributions. J Chem Inf Model (2009) 0.93

PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res (2011) 0.91

Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements. PLoS One (2010) 0.90

Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction. J Comput Aided Mol Des (2010) 0.88

Identification of ligand templates using local structure alignment for structure-based drug design. J Chem Inf Model (2012) 0.87

Mapping of ligand-binding cavities in proteins. Proteins (2010) 0.86

BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server. BMC Bioinformatics (2010) 0.84

Structural descriptor database: a new tool for sequence-based functional site prediction. BMC Bioinformatics (2008) 0.84

PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. Nucleic Acids Res (2014) 0.84

Bayesian refinement of protein functional site matching. BMC Bioinformatics (2007) 0.83

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development. J Comput Aided Mol Des (2009) 0.82

Rapid catalytic template searching as an enzyme function prediction procedure. PLoS One (2013) 0.82

Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. BMC Bioinformatics (2010) 0.81

Functional annotation strategy for protein structures. Bioinformation (2007) 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

Function prediction from networks of local evolutionary similarity in protein structure. BMC Bioinformatics (2013) 0.80

On the role of physics and evolution in dictating protein structure and function. Isr J Chem (2014) 0.79

A global optimization algorithm for protein surface alignment. BMC Bioinformatics (2010) 0.79

Local functional descriptors for surface comparison based binding prediction. BMC Bioinformatics (2012) 0.79

PESDserv: a server for high-throughput comparison of protein binding site surfaces. Bioinformatics (2010) 0.79

Similarity search for local protein structures at atomic resolution by exploiting a database management system. Biophysics (Nagoya-shi) (2007) 0.78

LigProf: a simple tool for in silico prediction of ligand-binding sites. J Mol Model (2007) 0.78

Protein surface matching by combining local and global geometric information. PLoS One (2012) 0.78

Regression applied to protein binding site prediction and comparison with classification. BMC Bioinformatics (2009) 0.78

Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. Protein Sci (2010) 0.77

A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations. PLoS One (2014) 0.77

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution. Biophysics (Nagoya-shi) (2012) 0.77

eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol (2014) 0.77

Ballast: a ball-based algorithm for structural motifs. J Comput Biol (2013) 0.77

Ligand binding site detection by local structure alignment and its performance complementarity. J Chem Inf Model (2013) 0.77

Exhaustive comparison and classification of ligand-binding surfaces in proteins. Protein Sci (2013) 0.76

Unstable argininosuccinate lyase in variant forms of the urea cycle disorder argininosuccinic aciduria. J Inherit Metab Dis (2015) 0.76

Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands. BMC Struct Biol (2012) 0.75

A simple method for finding a protein's ligand-binding pockets. BMC Struct Biol (2014) 0.75

Computing the protein binding sites. BMC Bioinformatics (2012) 0.75

G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design. Protein Sci (2016) 0.75

Local Alignment of Ligand Binding Sites in Proteins for Polypharmacology and Drug Repositioning. Methods Mol Biol (2017) 0.75

PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res (2005) 7.66

The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol (2009) 7.36

Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins (2002) 5.79

Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit. Science (2007) 5.19

Is allostery an intrinsic property of all dynamic proteins? Proteins (2004) 4.99

A method for simultaneous alignment of multiple protein structures. Proteins (2004) 3.45

Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A (2003) 3.42

Allostery: absence of a change in shape does not imply that allostery is not at play. J Mol Biol (2008) 3.24

Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol (2004) 3.10

Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects. Proc Natl Acad Sci U S A (2002) 3.06

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci (2002) 3.01

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci (2010) 2.97

Principles of protein-protein interactions: what are the preferred ways for proteins to interact? Chem Rev (2008) 2.96

FireDock: fast interaction refinement in molecular docking. Proteins (2007) 2.90

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64

Close-range electrostatic interactions in proteins. Chembiochem (2002) 2.42

FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res (2008) 2.39

The origin of allosteric functional modulation: multiple pre-existing pathways. Structure (2009) 2.33

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol Biosyst (2009) 2.18

Extended disordered proteins: targeting function with less scaffold. Trends Biochem Sci (2003) 2.12

A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci (2004) 2.11

PRISM: protein interactions by structural matching. Nucleic Acids Res (2005) 2.11

Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure (2004) 2.06

Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol (2006) 1.98

Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins (2003) 1.95

Geometry-based flexible and symmetric protein docking. Proteins (2005) 1.95

Flexible protein alignment and hinge detection. Proteins (2002) 1.93

Relationship between ion pair geometries and electrostatic strengths in proteins. Biophys J (2002) 1.91

HingeProt: automated prediction of hinges in protein structures. Proteins (2008) 1.86

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc (2011) 1.84

Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol (2008) 1.80

Principles of flexible protein-protein docking. Proteins (2008) 1.71

Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr Opin Chem Biol (2006) 1.70

ARTS: alignment of RNA tertiary structures. Bioinformatics (2005) 1.67

Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J Mol Biol (2004) 1.64

Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev (2010) 1.62

Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol (2010) 1.61

Similar binding sites and different partners: implications to shared proteins in cellular pathways. Structure (2007) 1.60

Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation. Protein Sci (2002) 1.59

Dynamic allostery: linkers are not merely flexible. Structure (2011) 1.58

Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. Proteins (2006) 1.58

Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. J Mol Biol (2004) 1.54

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res (2008) 1.52

Architectures and functional coverage of protein-protein interfaces. J Mol Biol (2008) 1.51

Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. J Mol Biol (2009) 1.48

Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome. Proc Natl Acad Sci U S A (2010) 1.48

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47

FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins (2010) 1.47

Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process. Biophys J (2007) 1.44

Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys J (2007) 1.44

New structures help the modeling of toxic amyloidbeta ion channels. Trends Biochem Sci (2008) 1.43

Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Proc Natl Acad Sci U S A (2005) 1.43

Atomic-level description of amyloid beta-dimer formation. J Am Chem Soc (2006) 1.41

The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res (2006) 1.37

Mechanisms of transcription factor selectivity. Trends Genet (2010) 1.35

Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys J (2003) 1.33

Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys J (2006) 1.33

Multiple structural alignment by secondary structures: algorithm and applications. Protein Sci (2003) 1.32

Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states. Proc Natl Acad Sci U S A (2010) 1.32

Allostery and population shift in drug discovery. Curr Opin Pharmacol (2010) 1.32

Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels. Biophys J (2008) 1.30

MolAxis: efficient and accurate identification of channels in macromolecules. Proteins (2008) 1.30

Nanoparticle-induced vascular blockade in human prostate cancer. Blood (2010) 1.30

Topological properties of protein interaction networks from a structural perspective. Biochem Soc Trans (2008) 1.28

The multiple common point set problem and its application to molecule binding pattern detection. J Comput Biol (2006) 1.28

Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy. J Am Chem Soc (2011) 1.27

Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach. Phys Biol (2005) 1.26

Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci (2006) 1.26

How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding. J Mol Biol (2006) 1.26

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics (2011) 1.25

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res (2010) 1.25

Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. Curr Med Chem (2004) 1.25

PRISM: protein-protein interaction prediction by structural matching. Methods Mol Biol (2008) 1.24

Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci (2009) 1.24

Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism. J Phys Chem B (2009) 1.23

Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol (2007) 1.22

Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets. Nucleic Acids Res (2007) 1.22

β-Barrel topology of Alzheimer's β-amyloid ion channels. J Mol Biol (2010) 1.21

How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J (2004) 1.21

SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res (2005) 1.20