A survey of available tools and web servers for analysis of protein-protein interactions and interfaces.

PubWeight™: 1.47‹?› | Rank: Top 5%

🔗 View Article (PMC 2671387)

Published in Brief Bioinform on February 24, 2009

Authors

Nurcan Tuncbag1, Gozde Kar, Ozlem Keskin, Attila Gursoy, Ruth Nussinov

Author Affiliations

1: Computational Sciences and Engineering Program at Koc University, Istanbul, Turkey.

Articles citing this

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics (2010) 1.72

ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery. Nucleic Acids Res (2010) 1.28

PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res (2011) 1.25

Computational prediction of protein hot spot residues. Curr Pharm Des (2012) 1.11

Integrative approaches to the prediction of protein functions based on the feature selection. BMC Bioinformatics (2009) 1.01

Amyloidogenic regions and interaction surfaces overlap in globular proteins related to conformational diseases. PLoS Comput Biol (2009) 0.94

PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. Nucleic Acids Res (2012) 0.93

Predicting protein-protein interface residues using local surface structural similarity. BMC Bioinformatics (2012) 0.93

Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface. J Am Chem Soc (2013) 0.91

Flexibility and small pockets at protein-protein interfaces: New insights into druggability. Prog Biophys Mol Biol (2015) 0.90

Roles of residues in the interface of transient protein-protein complexes before complexation. Sci Rep (2012) 0.90

Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. Mol Inform (2014) 0.90

DockRank: ranking docked conformations using partner-specific sequence homology-based protein interface prediction. Proteins (2013) 0.85

Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts. BMC Bioinformatics (2014) 0.84

Beta atomic contacts: identifying critical specific contacts in protein binding interfaces. PLoS One (2013) 0.84

Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective. BMC Bioinformatics (2010) 0.84

Tools used to study how protein complexes are assembled in signaling cascades. Bioeng Bugs (2011) 0.83

Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. Curr Genomics (2013) 0.81

Algorithmic approaches to protein-protein interaction site prediction. Algorithms Mol Biol (2015) 0.81

Progress and challenges in predicting protein interfaces. Brief Bioinform (2015) 0.81

Prediction of contact matrix for protein-protein interaction. Bioinformatics (2013) 0.80

Hot spots in a network of functional sites. PLoS One (2013) 0.80

KBDOCK 2013: a spatial classification of 3D protein domain family interactions. Nucleic Acids Res (2013) 0.79

Improved multi-level protein-protein interaction prediction with semantic-based regularization. BMC Bioinformatics (2014) 0.78

Local network patterns in protein-protein interfaces. PLoS One (2013) 0.78

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

Beta-strand interfaces of non-dimeric protein oligomers are characterized by scattered charged residue patterns. PLoS One (2012) 0.76

Ranking Docked Models of Protein-Protein Complexes Using Predicted Partner-Specific Protein-Protein Interfaces: A Preliminary Study. ACM BCB (2011) 0.76

Ens-PPI: A Novel Ensemble Classifier for Predicting the Interactions of Proteins Using Autocovariance Transformation from PSSM. Biomed Res Int (2016) 0.76

Modeling amyloid-beta as homogeneous dodecamers and in complex with cellular prion protein. PLoS One (2012) 0.76

Integrated web visualizations for protein-protein interaction databases. BMC Bioinformatics (2015) 0.76

Intermolecular β-strand networks avoid hub residues and favor low interconnectedness: a potential protection mechanism against chain dissociation upon mutation. PLoS One (2014) 0.75

PBSword: a web server for searching similar protein-protein binding sites. Nucleic Acids Res (2012) 0.75

Selecting temperature for protein crystallization screens using the temperature dependence of the second virial coefficient. PLoS One (2011) 0.75

Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. BMC Bioinformatics (2015) 0.75

AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking. BMC Bioinformatics (2017) 0.75

Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues. J Chem Inf Model (2012) 0.75

CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys. PLoS One (2016) 0.75

Intensification: A resource for amplifying population-genetic signals with protein repeats. J Mol Biol (2016) 0.75

In Silico Structure-Based Approaches to Discover Protein-Protein Interaction-Targeting Drugs. Methods (2017) 0.75

Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms. Curr Opin Toxicol (2017) 0.75

Articles cited by this

(truncated to the top 100)

Initial sequencing and analysis of the human genome. Nature (2001) 212.86

Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97

The Protein Data Bank. Nucleic Acids Res (2000) 187.10

VMD: visual molecular dynamics. J Mol Graph (1996) 117.02

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 47.15

Inference of macromolecular assemblies from crystalline state. J Mol Biol (2007) 44.95

A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A (2001) 33.71

A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol (1999) 25.13

Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science (2001) 24.48

BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng (1995) 19.22

BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res (2003) 18.75

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res (2002) 15.70

IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02

Principles of protein-protein interactions. Proc Natl Acad Sci U S A (1996) 14.51

The atomic structure of protein-protein recognition sites. J Mol Biol (1999) 12.63

PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res (2001) 12.21

STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res (2006) 12.16

MIPS: a database for genomes and protein sequences. Nucleic Acids Res (2002) 11.98

MINT: the Molecular INTeraction database. Nucleic Acids Res (2006) 11.90

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc (2003) 11.65

Printing proteins as microarrays for high-throughput function determination. Science (2000) 10.77

Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science (1985) 10.42

A hot spot of binding energy in a hormone-receptor interface. Science (1995) 10.41

Shape complementarity at protein/protein interfaces. J Mol Biol (1993) 10.40

Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res (2004) 9.99

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74

Anatomy of hot spots in protein interfaces. J Mol Biol (1998) 9.70

PQS: a protein quaternary structure file server. Trends Biochem Sci (1998) 9.24

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res (2006) 9.19

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics (2003) 7.83

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

Online predicted human interaction database. Bioinformatics (2005) 6.83

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics (2005) 6.82

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph (1995) 6.64

Principles of protein-protein recognition. Nature (1975) 6.50

The FoldX web server: an online force field. Nucleic Acids Res (2005) 6.30

A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci U S A (2002) 6.18

Unraveling hot spots in binding interfaces: progress and challenges. Curr Opin Struct Biol (2002) 6.06

ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res (2005) 5.79

An in vivo map of the yeast protein interactome. Science (2008) 5.52

Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol (1997) 4.69

Scoring residue conservation. Proteins (2002) 4.66

Electrostatic aspects of protein-protein interactions. Curr Opin Struct Biol (2000) 4.57

The structure of protein-protein recognition sites. J Biol Chem (1990) 4.55

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

Dissecting protein-protein recognition sites. Proteins (2002) 4.51

Analysis of protein-protein interaction sites using surface patches. J Mol Biol (1997) 4.51

ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res (2004) 4.10

GRAMM-X public web server for protein-protein docking. Nucleic Acids Res (2006) 3.71

Protein docking using spherical polar Fourier correlations. Proteins (2000) 3.60

Protein docking using continuum electrostatics and geometric fit. Protein Eng (2001) 3.48

The RosettaDock server for local protein-protein docking. Nucleic Acids Res (2008) 3.48

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

Computational alanine scanning of protein-protein interfaces. Sci STKE (2004) 3.41

ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol (2004) 3.18

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

PIC: Protein Interactions Calculator. Nucleic Acids Res (2007) 3.02

Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci (1997) 3.00

Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins (2001) 3.00

Analysing six types of protein-protein interfaces. J Mol Biol (2003) 2.96

Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins (2002) 2.95

Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics (2004) 2.93

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

A protein-protein docking benchmark. Proteins (2003) 2.90

Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol (2007) 2.84

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res (2006) 2.81

ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics (2001) 2.60

Protein-protein interaction at crystal contacts. Proteins (1995) 2.50

Annotating nucleic acid-binding function based on protein structure. J Mol Biol (2003) 2.46

Conservation of polar residues as hot spots at protein interfaces. Proteins (2000) 2.42

PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics (2005) 2.39

Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci (2004) 2.38

Anchor residues in protein-protein interactions. Proc Natl Acad Sci U S A (2004) 2.35

Recognition of functional sites in protein structures. J Mol Biol (2004) 2.32

Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol (1998) 2.30

Dissecting subunit interfaces in homodimeric proteins. Proteins (2003) 2.24

Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins (2001) 2.21

Protein binding site prediction using an empirical scoring function. Nucleic Acids Res (2006) 2.19

3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res (2005) 2.18

An investigation of protein subunit and domain interfaces. Protein Eng (1988) 2.18

Specific versus non-specific contacts in protein crystals. Nat Struct Biol (1997) 2.15

Protein-protein interaction hotspots carved into sequences. PLoS Comput Biol (2007) 2.15

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

An in vivo library-versus-library selection of optimized protein-protein interactions. Nat Biotechnol (1999) 2.09

A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol (1996) 2.07

SCOPPI: a structural classification of protein-protein interfaces. Nucleic Acids Res (2006) 2.06

Dynamic properties of the Ras switch I region and its importance for binding to effectors. Proc Natl Acad Sci U S A (2001) 1.99

Conservation helps to identify biologically relevant crystal contacts. J Mol Biol (2001) 1.98

Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res (2005) 1.95

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

Prediction-based fingerprints of protein-protein interactions. Proteins (2007) 1.92

Analysis of protein interactions using fluorescence technologies. Curr Opin Chem Biol (2003) 1.91

firestar--prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res (2007) 1.91

SPR for molecular interaction analysis: a review of emerging application areas. J Mol Recognit (2004) 1.90

Protein-protein crystal-packing contacts. Protein Sci (1997) 1.89

Protein binding versus protein folding: the role of hydrophilic bridges in protein associations. J Mol Biol (1997) 1.86

Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics (2005) 1.86

NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics (2006) 1.85

Articles by these authors

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

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

Recognition of functional sites in protein structures. J Mol Biol (2004) 2.32

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

Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics (2005) 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

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics (2009) 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

Human cancer protein-protein interaction network: a structural perspective. PLoS Comput Biol (2009) 1.54

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

HotSprint: database of computational hot spots in protein interfaces. Nucleic Acids Res (2007) 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

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

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

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

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

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

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

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

HotPoint: hot spot prediction server for protein interfaces. Nucleic Acids Res (2010) 1.30

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

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

Oxidative stress and genetic and epidemiologic determinants of oxidant injury in childhood asthma. J Allergy Clin Immunol (2006) 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

Transient protein-protein interactions. Protein Eng Des Sel (2011) 1.22