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PPI hotspots, PPI ligands, Interface residues

 

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Protein WISDOM The framework is divided into two stages: a sequence selection stage and a validation stage. The sequence selection stage designs novel protein and peptide sequences based upon a rigid or flexible design template uploaded by the user. Once sequence are generated, they can be validated by either fold specificity or approximate binding affinity. Fold specificity is a measure of how well the designed sequence adopts the template fold while approximate binding affinity is a measure of how well the designed sequence binds to a given protein target online
BindUP Non-homology-based prediction of DNA and RNA binding proteins online
PinaColada Design of protein-protein interaction (PPI) inhibitors is a major challenge in Structural Bioinformatics. Peptides are natural candidates for inhibition of protein-protein complexes. PinaColada, a novel computational method for the design of peptide inhibitors for protein-protein interactions (2016) online
MoRFchibi Tools for the identification of MoRFs (short segments within longer disordered protein regions that bind to globular protein domains in a process known as disorder-to-order transition) in protein sequences (2016) online
iFraG A protein–protein interface prediction server based on sequence fragments (2016) online
HotSpot HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design of smart libraries for engineering proteins’ stability, catalytic activity, substrate specificity and enantioselectivity. The server integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools (2016) online
Mechismo Predicting the mechanistic impact of mutations and modifications on molecular interactions (protein-protein, PPi) online
MutaBind Estimates and interprets the effects of sequence variants on protein–protein interactions online
iPPBS-Opt A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by Optimizing Imbalanced Training Datasets (2016) online
PrePPItar With the booming of interactome studies, a lot of interactions can be measured in a high throughput way and large scale datasets are available. It is becoming apparent that many different types of interactions can be potential drug targets. Compared with inhibition of a single protein, inhibition of protein–protein interaction (PPI) is promising to improve the specificity with fewer adverse side-effects. Also it greatly broadens the drug target search space, which makes the drug target discovery difficult. Machine learning method to predict PPI targets in a genomic-wide scale online
MolStructPred Solvent Accessible Surface Area-Based Hot-Spot Detection Methods for Protein–Protein and Protein–Nucleic Acid Interfaces (2015). SASA-HS-PNA, SASA-HS-PP online
AlphaSpace Fragment-Centric Topographical Mapping to Target Protein-Protein Interaction Interfaces (2015) standalone
PSIVER PSIVER is a server for the prediction of protein-protein interaction sites in protein sequences online
I-COMS Interprotein-COrrelated Mutations Server. Allows to estimate covariation between residues of different proteins by four different covariation methods. Results might be used to prioritize protein positions in a mutation analysis based on their inter and intra (if part of a complex) coevolutionary role. It might also provide a guide for docking experiments and to gain insights into protein–protein interaction when a structure of the complex is not available online
jsPISA Analysis of macromolecular interfaces and identification of biological assemblies (complexes) from macromolecular crystal structures (2015) online
CompASM Computational Alanine Scanning Mutagenesis presents here as a very intuitive plug-in for two widely distributed software (AMBER and Visual Molecular Dynamics – VMD) that allows the user to perform a full Alanine Scanning Mutagenesis (ASM) procedure, requiring only very little user effort. It is composed of two main packages: the Core and Graphical User Interface (GUI) standalone
Profppikernel Evolutionary profiles improve protein–protein interaction prediction from sequence standalone
Ccharppi Computational Characterisation of Protein-Protein Interactions online
Structure-PPi A module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. The Structure-PPi system for the comprehensive analysis of coding SNVs based on 3D protein structures of protein complexes. The 3D repository used, Interactome3D, includes experimental and modeled structures for proteins and protein-protein complexes. Structure-PPi annotates SNVs with features extracted from UniProt, InterPro, APPRIS, dbNSFP, and COSMIC databases standalone
PPI tool 3D Complex is a hierarchical classification of protein complexes that describes similarities in structure, sequence, as well as topology of contacts of the constituent proteins online
Mutation tool Inferring the microscopic surface energy of protein-protein interfaces from mutation data (2015) online
CONSRANK A server for the analysis, comparison and ranking of docking models based on inter-residue contacts Online
CRF CRF-based models of protein surfaces improve protein-protein interaction site predictions Online
eFindSitePPI The tool detects protein binding sites and residues using meta-threading. It also predicts interfacial geometry and specific interactions stabilizing protein-protein complexes, such as hydrogen bonds, salt bridges, aromatic and hydrophobic interactions Online and standalone
mcsm-ppi Protein-Protein Affinity Change Upon Mutation Online
iAlign Structural comparison of protein-protein interfaces standalone
CCharPPI CCharPPI calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions online
PPA_Pred Protein-protein binding affinity prediction from amino acid sequence online
LoopFinder for PPI cmpd design A web-based interface for LoopFinder is currently under construction. In the meantime, LoopFinder is freely available for use. Requests for binary files or code can be sent to This email address is being protected from spambots. You need JavaScript enabled to view it. (Gavenonis et al, Nat Chem Biol. 2014) standalone for now
PPI-Server The classification of protein-protein interactions into permanent, transient and crystal artifacts is still an unsolved problem. This server investigates this question online
EPPIC Evolutionary Protein Protein Interface Classifier (Duarte et al, BMC Bioinformatics, 2012) aims at distinguishing biologically relevant interfaces from crystal contacts in protein crystal structures. The approach was also successfully used in Dr. Capitani's lab to investigate oligomerization interfaces in transmembrane proteins online
COCOMAPS bioCOmplexes COntact MAPS is a web application to easily and effectively analyse and visualize the interface in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes), by making use of intermolecular contact maps online
PredHS A web server for predicting protein–protein interaction hot spots by using structural neighborhood properties online
CAD-score The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes online
PredictProtein Open resource for online prediction of protein structural and functional features. A meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein–protein binding sites (ISIS2), protein–polynucleotide binding sites (SomeNA) and predictions of the effect of SNPs on protein function (SNAP2) online
DoReMi Context-based prioritization of linear motif matches online
PSIPRED and HSPred Hotspot predictions online
Rosetta Rosettacommons, protocols to design oxopiperazine helix mimetics and other peptides for PPI online
AquaProt AquaProt analyses protein-protein binding interface, defines inter-residue interaction map within the interface and extracts related water molecules online
VASCo VASCo is a program pipeline including a visualization tool to calculate and visualize annotated surfaces with special emphasis on surface contact regions and protein-protein interactions standalone
hotspot predictors Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences standalone
SEQMOL SEQMOL is a PDB structure analysis suite. It can be used to align multiple protein and DNA sequences, compute evolutionary attributes of multiple sequence alignments (such as sequence conservation, hydrophobicity conservation, conformational flexibility conservation, physical covariation, protein-protein interface (has the ODA tool and Conservation of protein-protein interaction propensity), Nucleic acid desolvation analysis, protein-RNA interface and protein-DNA interface propensity (Predicting protein-RNA binding sites via residue interface propensity conservation with subsequent patch energy calculation), and conservations thereof) and to map these features onto PDB files. Many of the features do not use multiple sequence alignment and directly analyze PDB coordinates to yield insights that could often be valuable. Binding constants prediction module for PDB complexes and crystal contacts based on a de-novo built algorithm with sound Kd accuracy Kd predictions in SEQMOL are user-friendly and usually fast (seconds-minutes for average-sized complexes on a local CPU). A PDB file is DragDropped onto the application. Kd along with a comprehensive interface analysis is produced in the output. For multiple-PDB jobs, such as scoring of decoys from docking programs, batch PDB processing is done automatically if more than one PDB was DragDropped standalone
HotPatch HotPatch finds unusual patches on the surface of proteins, and computes just how unusual they are (patch rareness), and how likely each patch is to be of functional importance online
ET-viewer ET viewer: an application for predicting and visualizing functional sites in protein structures. The Evolutionary Trace Viewer (ETV) provides a one-stop environment in which to run, visualize and interpret Evolutionary Trace (ET) predictions of functional sites in protein structures online
DoBi Find binding sites and can be used for docking standalone
TreeDet Predicting Functional Residues in Protein Sequence Alignments. (help to predict interface residues, co-evolution) standalone
Patch Finder Plus (PFplus) A web server for extracting and displaying positive electrostatic patches on protein surfaces online
Crescendo Crescendo is a program for identifying functional sites in proteins. It distinguishes structural and functional restraints in evolution in order to identify interaction sites online
HADDOCK2P2I A robust biophysical model for predicting the binding affinity of protein-protein interaction inhibitors online
surface triplet propensities or STP Identification of protein binding surfaces using surface triplet propensities. The method described here does not explicitly look for cavities but uses small surface patches consisting of triplets of adjacent surface atomic groups that can be touched simultaneously by a probe sphere representing a solvent molecule online
FragVLib FragVLib a free database mining software for generating Fragment-based Virtual Library using pocket similarity search of ligand-receptor complexes. A free software which is developed as a tool for performing similarity search across database(s) of ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor standalone
PAIRpred Partner-specific prediction of interacting residues from sequence and structure python scripts
MMDB and VAST+ Tracking structural similarities between macromolecular complexes online
iPred Protein-Protein Interface and Hot-Spot Prediction online
MetaPPI A meta approach to predict protein-protein interaction binding site, combines PPI-PRED, PPISP, PINUP, Promate, SPPIDER online
PRICE Energetics of PPI interfaces - conservations online
RosettaBackrub Flexible backbone protein structure modeling and design server. Can be used for Point mutation, Backbone ensemble (creates near-native structural ensembles), Sequence tolerance (predicts sequences tolerated for proteins and protein-protein interfaces using flexible backbone design methods. Example applications are the generation of sequence libraries for experimental screening and prediction of protein or peptide interaction specificity) online
PATRIC PATRIC, the bacterial bioinformatics database and analysis resource online
EleKit EleKit allows to measure the similarity of electrostatic potentials between a docked small molecule and a known ligand protein for the same receptor. EleKit is intended to facilitate the design of SMPPIIs (Small Molecule Protein-Protein Interaction Inhibitors) standalone
HOMOLOBIND HOMOLOBIND identifies residues in protein sequences with significant similarity to structurally characterized binding sites online
PPIcons PPIcons: identification of protein-protein interaction sites in selected organisms standalone
SPPIDER SPPIDER prediction of PPI binding sites (use 3D structure or sequence) online
Dsppi Dsppi : Drugscore-PPI is a knowledge-based scoring function for computational alanine-scanning in protein-protein interfaces online
Score-MI An information-theoretic classification of amino acids for the assessment of interfaces in protein-protein docking. The reduced alphabets derived from the present work were converted into a scoring function for the evaluation of docking solutions, which is available for public use via the web service score-MI online scoring
PPIevo PPIevo: Protein-protein interaction prediction from PSSM based evolutionary information standalone
PPI Affinity prediction Protein-protein binding affinity prediction on a diverse set of structures online
PPI prediction PPI Prediction Server classifies a protein-protein complex concerning its interaction type into permanent, transient or crystal artifact. The discrimination is performed using two characteristics of the protein-protein complex, the hydrophobicity of the interface and the quotient of interface area ratios online
LINK BeAtMuSiC : prediction of changes in protein-protein binding affinity on mutations online
dPred A program to calculate the desolvation penalties of small probes in cavities to identify possible binding sites of small ligands standalone
Proface Analysis of protein-protein interface online online
PI2PE Protein interface-interior prediction engine online
3D-Surfer Offers web-based tools for rapid protein surface analysis and comparison. The server integrates various methods to assist in the high throughput screening and visualization of protein surface comparisons online
InterProSurf Protein-Protein Interaction Server online online
Intervor Investigating MacroMolecular Interfaces online
PDBePISA Protein Interfaces, Surfaces and Assemblies online
BIPS BIANA Interolog Prediction Server. A tool for protein-protein interaction inference online
I2I-SiteEngine Structural and Physico-Chemical Alignment of Protein-Protein Interfaces online
DiMoVo DIscriminate between Multimers and MOnomers by VOronoi tessellation online
Dr PIAS Druggable Protein-protein Interaction Assessment System Protein-protein interaction PPI
JCB Numerous information and links: protein interaction network and databases of complexes can be found at the JCB Protein-Protein Interaction Website links and tools for macromolecular interactions
MolSurfer  A macromolecular interface navigator  Interface analysis standalone and online
LINK Biomolecular modelling group: several tools for PPIs online and standalone
AquaSAXS A web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models online
Drug-SNPing An integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping All drug-based and protein-protein interaction-based SNP genotyping information are provided with PCR-RFLP (PCR-restriction enzyme length polymorphism) and TaqMan probes online
PS-HomPPI  A sequence-based partner-specific protein-protein interface residue prediction server online
NPS-HomPPI  A sequence-based non-partner-specific protein-protein interface residue prediction server online
PBSword  A web server designed for efficient and accurate comparisons and searches of geometrically similar protein-protein binding sites from a large-scale database online
SynSysNet Based on an expert-curated list of 1.000 human genes, specific to the synapse. Information on resulting proteins, their 3D structure, binding small molecules Protein-Protein-Interactions (PPIs) and Compound-Protein-Interactions are integrated online
DOMINO  An open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains  database
SNAPPI  Structures, iNterfaces and Alignments for Protein-Protein Interactions SNAPPI-DB is a database of domain-domain interactions SNAPPI-Predict is a protein-protein interaction prediction program which is currently in development SNAPPI-View is the web interface to SNAPPI-DB and SNAPPI-Predict online
InterEvScore A novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution standalone
PPISURV A novel bioinformatics tool for uncovering the hidden role of specific genes in cancer survival outcome online PPI online
NETAL A new graph-based method for global alignment of protein-protein interaction networks standalone Binaries supported linux
PredUs Prediction of Protein Interfaces Using Structural Alignment online
KBDOCK  3D database system that defines and spatially clusters protein binding sites for knowledge-based protein docking. KBDOCK integrates protein domain-domain interaction information from 3DID and sequence alignments from PFAM together with structural information from the PDB in order to analyse the spatial arrangements of DDIs by Pfam family, and to propose structural templates for protein docking Database PPI
iLoops Uses protein structural features (loops and domains) of interacting and non-interacting protein pairs to determine whether any pair of proteins interacts or not online
CSPred-PPI Combines a compressed sensing (CS) algorithm and support vector machines to predict Saccharomyces cerevisiae PPIs from primary sequence online
CD A sequence-based co-evolutionary divergence (CD) method for PPIs prediction in the human proteome standalone
ISMBLab_PPI A machine-learning algorithm that predicts PPIs sites based on the distribution of physicochemical complementarity features of non-covalent interacting atoms in protein surfaces online
iWRAP  Predicts PPIs and their interfaces based on a protein interface threading approach online
P.R.I.S.M. A web-server that can be used to explore protein interfaces and predict protein-protein interactions (PRISM). The server is now server is out of service and not up-to-date online
HotRegion HotRegion: a database of predicted hot spot clusters database
CMA Contact Map Analysis (CMA) webserver. This program allows to analyse contacts between two chains or within one chain in a given PDB file online
PCRPi-W Presaging Critical Residues in Protein interfaces-Web Server (PCRPi-W): A Web Server to Chart Hot Spots in Protein Interfaces online
BioCreAtIvE Community-wide assessment of text mining methods .
SGI Second generation structural genomics initiatives focus on protein complexes .
Trypano-PPI A web server for prediction of unique targets in trypanosome proteome online
PCRPi Presaging Critical Residues in Protein interfaces-Web server implements a recently described and highly accurate computational tool designed to predict critical residues in protein interfaces online
CPORT  An algorithm for the prediction of protein-protein interface residues online
PIC Protein Interactions Calculator Protein-protein energy computation, online, structural analysis
DrugscorePPI  A knowledge-based scoring function for computational alanine-scanning in protein-protein interfaces       Hot-Spots online
ANCHOR  A web-based tool whose aim is to facilitate the analysis of protein-protein interfaces with regard to its suitability for small molecule drug design        Hot-Spots online
KFC     KFC Server: interactive forecasting of protein interaction hot spots              Hot-Spots online
HotSprint     Database of computational hot spots in protein interfaces   Hot-Spots
Prism Prism Protocol Binding site analysis, prediction, standalone
FastContact A free energy scoring tool for protein protein complex structures Macromolecular scoring (PPI) online
PIER Prediction of interfaces based on atomic statistical propensities online
SPA-PP Scoring function, specificity and affinity of the protein-protein interactions (algorithm is implemented in C language Bioinformatics, 2013 29:1127-33) standalone
meta-PPISP Meta server for interface prediction using cons- PPISP, PINUP and Promate online
pyDockNIP Prediction of binding hot-spots from docking. pyDock module ODA could be use to predict interface regions online
FTMap Computational solvent mapping is a powerful tool to understand interactions between proteins and solvent molecules. It docks small organic molecules on a protein surface, finds favorable binding positions, clusters the conformations of all prediction, and ranks the clusters on the basis of their average free energy. The low energy clusters are grouped into consensus sites and the largest consensus sites are of interest. The docked fragments can also be served as the building blocks for fragment-based drug design. There is an option to turn on for PPI interaction online
FOLDEF Energy-based alanine-scanning of a protein complex structure online
HotPoint Prediction of binding hot-spots based on accessibility and knowledge-based potentials hotspot
ISIS Sequence-based neural network method for prediciton of binding hot-spot residues and interface residues (first for interface residues but can help for hotspots) .
ROBETTA Should be able to do Ala scan for hotspot predictions .
KFC2 The original KFC Server (Knowledge-based FADE and Contacts) predicted binding hotspots within protein-protein interfaces by recognizing structural features indicative of important binding contacts is now KFC2 (with option of Rosetta Ala scan) (need structure of the complex) .
MAPPIS Recognizes spatially conserved chemical interactions shared by a set of PPIs (needs 3D structure) Multiple Alignment of Protein-Protein InterfaceS (PPIs). (Evolutionary conservation, the tool aims to analyze protein-protein interactions) .
pyDockNIP pyDockNIP predict hotspots using 2 unbound protein structures via the pyDock tool standalone
ProMate Prediction of potential protein-protein binding sites for unbound proteins Binding site prediction online
WHISCY  interface prediction based on conservation and surface properties online
ODA ODA (Optimal Docking Areas), the server is possibly down, please contact Molsoft Binding site prediction online
LINK PPI databases, tools many links .
PLATINUM  Designed for calculation of hydrophobic properties of molecules and their match or mismatch in receptor-ligand complexes. These properties may help to analyze results of molecular docking .
PresCont Predicting protein-protein interfaces utilizing four residue properties .
LINK Analysis of interatomic Contacts in Ligand-Protein complexes Analysis of interatomic contacts in protein entries Analysis of interatomic Contacts
SCOWLP  A web-based relational database formed by eleven tables describing PDB interface interactions. The new update also includes 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds Interfaces - databases online
ADP_EM Makes it possible to accurately dock atomic structures into low-resolution electron-density maps Docking in electron-density maps derived from for instance electron microscopy standalone
FADE See also  The Fast Atomic Density Evaluator (FADE) and Pairwise Atomic Density Reverse Engineering (PADRE). Many tools Predict binding sites and analyze docked complexes
3did  A collection of domain-domain interaction structures and catalogue of domain-peptide structural motifs in the PDB online
HotSpot Wizard A web server for identification of hot spots online
ConSurf Enables the identification of functionally important regions on the surface of a protein or domain, of known three-dimensional (3D) structure, based on the phylogenetic relations between its close sequence homologues online
Rate4Site Detects conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment standalone
Firestar  Prediction of functionally important residues  online
2P2I The 2P2I Database, list of complexes and druggability prediction of the interface  online
PPI-HitProfiler In silico filter to build a compound collection enriched in PPI inhibitors (CDithem) standalone and online via FAF-Drugs3
iPPI-DB  Contains 1600 non-peptidic inhibitors (iPPI) accross 12 classes of protein-protein interactions (PPI). The chemical structures of iPPI are manually extracted from the literature (peer-reviewed articles or world patents) along with their phamacological profile and store in iPPI-DB (CDithem project) curated database
TIMBAL Atomic Interactions and Profile of Small Molecules Disrupting PPI Interfaces: the TIMBAL Database  database
AnchorQuery  Is a specialized  pharmacophore  search technology that brings interactive virtual screening of novel protein-protein inhibitors to the desktop Protein-protein inhibitors online
ProMateus An open research approach to protein-binding sites analysis Mutation and docking/binding online
HyPare  Tool based on the PARE algorithm (Predicting Association Rate Enhancement). With HyPare you can find hotspots for association, and thus, engineer molecules... Mutation and docking/binding online
OCA A browser-database for protein structure/function Structural Analysis, online
PARE The program calculates the change in rate of association (kon) of mutant protein-protein interaction complexes from the change in the Debye Huckel energy of interaction Structural Analysis, binding, mutations, online
NOXclass Prediction of protein-protein interaction types (biological obligate, biological non-obligate and crystal packing) implemented using a support vector machine (SVM) algorithm online
DILIMOT A server for finding short (3-8 amino acids), over-represented peptide patterns, or Linear motifs, in a set of proteins online
SLiMFinder A web server to find novel, significantly over-represented, short protein motifs online
ELM A computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional site prediction using as input aa sequence. Can be used to search PPI online
PIE PIE (Protein Interaction information Extraction) information about PPI