Web Servers

Webservers related to protein structure prediction and analysis

   Name of webservers                         Description   Category
WHAT IFThis server find structural problems in PDB entries that have been determined using X-ray diffraction or NMR techniques.Protein verification tool
pdb-careIt aids experimentalists in detecting discrepancies in connectivities and nomenclature.Detect error in PDB entries.
CPHModelsThis method is homology modeling software and is based on profile alignment guided by secondary structure and exposure prediction.Protein structure prediction
SWISS-MODELThis method is a fully automated homology modeling server used for iprotein structure prediction.Protein structure prediction
WHAT_CHECKIt is a refinement tool for PDB, it finds incorrect structure.Protein verification tool
3vee3vee is collection of program for the assessment of volumes in protein files.Protein Volume assessment
3DLigandSite3DLigandSite is an automated method for the prediction of ligand binding sites.Protein binding site prediction
IntFOLDThe IntFOLD server provides a unified interface for, Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction and Prediction of protein-ligand binding residues.Protein structure and function prediction
firestarfirestar server: predicting functional residues from structural templates and alignment reliability.Prediction of functional residues
SA-MotIt extract structural motifs from protein loop structures using HMM-SA.Extract structural motifs
CSpritzCSpritz server predict Disorder region in proteins.Protein disorder prediction
NetTurnP 1.0NetTurnP server predict Beta-turn regions in protein sequences.Protein structure prediction
NetSurfP ver. 1.1NetSurfP ver. 1.1 - Protein Surface Accessibility and Secondary Structure Predictions.Protein structure prediction
SCRATCHProtein structure prediction including various related servers.Protein structure prediction
BETAproThe Server of Predicting Beta-Residue Pair, Strand Pair, Strand Alignment, and Beta-Sheet Architecture.Protein structure prediction
TMBproTransmembrane Beta-Barrel Secondary Structure, Beta-Contact, and Tertiary Structure Predictor.Protein structure prediction
SIDEproSIDEpro is a novel machine learning approach for the fast and accurate prediction of side-chain conformations.Protein structure prediction
APSSP2This server allow to predict the secondary structure of protein's from their amino acid sequence. This is an advanced version of our PSSP server, which participated in CASP3 and in CASP4.Protein Structure Prediction
PROTEUS2PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation.Protein Structure prediction
BetaTPred3The server is developed for predicting beta turns based on propensity score.Protein Structure Prediction
BetaTurnsBetaturns server is to predict different types of turns such as Types I, II, IV, VIII and non-specific in a given amino acid sequence.Protein Structure Prediction
PORTERPorter: a new, accurate server for protein secondary structure prediction.Protein secondary structure prediction
PPCpredThis server is designed for sequence-based prediction of protein crystallization, purification, and production propensity.prediction of Protein crystallization
YASPINA simple and fast secondary structure prediction method using hidden neural networks.Protein secondary structure prediction
SARpredSARpred is a ANN based computational method for predicting protein surface accessibility. Prediction of surface accessibility
SANNSANN is nearest neighbor based method developed for predicting protein surface accessibility. Prediction of surface accessibility
PSIPREDServer utilizes evolutionary information in form of alignment profile for structure predictionProtein secondary structure prediction
SOPMAMethod is based on protein family alignment profile for structure predictionProtein secondary structure prediction
AlphaPredThe AlphaPred server predicts the alpha turn residues in the protein sequence.Protein Structure Prediction
HSPredHSPred is a computational method to predict hot spot residues at protein-protein interfaces. It is based on Support Vector Machines (SVM) and on calculated energy potentials. Prediction of protein-protein interactions
GammaPredThe GammaPred server predicts the gamma turn residues in the protein sequence.Protein Structure Prediction
BhairPredBhairPred is a server that predicts the beta hairpins in the protein sequence.Protein Structure Prediction
Paircoil The Paircoil program predicts the location of coiled-coil regions in amino acid sequences.Primary structure analysis
MulticoilThe MultiCoil program predicts the location of coiled-coil regions in amino acid sequences and classifies the predictions as dimeric or trimeric. Primary structure analysis
CFSSPThis server predicts secondary structure of protein from the amino acid sequence.Secondary structure prediction
PREDATORMethod based on hydrogen bonded residues in a single amino acid sequenceProtein secondary structure prediction
Jpred4A consensus method for protein secondary structure prediction at University of DundeeSecondary structure prediction
STRAPThe free computer program STRAP aligns proteins by sequence and 3D-structure.Tertiary structure analysis
TopMatch-webProtein structure comparisonTertiary structure analysis
3DjigsawThree-dimensional models for proteins based on homologues of known structureTertiary structure prediction
Geno3dAutomatic modelling of protein three-dimensional structureTertiary structure prediction
Phyre2Automated 3D model building using profile-profile matching and secondary structureProtein structure prediction
ITASSERSoftware for protein structure prediction using threading approachProtein structure prediction
ROBETTAComparative and de novo approcah based structure prediction softwareProtein structure prediction
QUARKAb inition based protein folding and structure prediction softwareProtein folding and structure prediction
Bhageerath-HHomology and ab initio approcah based structure prediction softwareProtein structure prediction
MODELLERHomology and comparative modeling based approcah for structure predictionProtein structure prediction
GalaxyWEBSuite for protein structure prediction, refinement and interaction softwareProtein structure prediction, refinement and interaction
SCRATCHComplete package for protein analysisProtein structure analysis
MULTICOMMethod utilizes information from multiple sources for building modelsProtein structure prediction
ModWebTemplate based structure prediction softwareProtein structure prediction
PS2Protein structure prediction software which uses comparative modeling approachProtein structure prediction
RaptorXNonlinear scoring function for predicting structure of non-homologous proteinsProtein structure prediction
HMMSTR/Rosetta Prediction of protein structure from sequenceTertiary structure prediction
EDSThe Uppsala Electron Density Server (EDS) provides the scientific community with a service for evaluating the electron density of crystal structures deposited in the Protein Data Bank.Evaluating the electron density of crystal structures
FATCATFlexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) is a flexible protein structure comparison algorithm.Structure Alignment and Comparison
QMEANclustQMEANclust perform estimation of protein model quality by combining a composite scoring function with structural density information.Protein Structure Quality Assessment
PconsPcons is a Protein Structure Prediction Meta Server.Protein Structure Prediction
ModFOLDclustThis server for predicting the quality of three-dimensional (3D) models is fundamentally important for the success of tertiary structure (TS) prediction strategies.Protein Structure Quality Assessment
MUFOLD-WQAIt is method for quality assessment in protein structure prediction.Protein Structure Quality Assessment
ESyPred3DESyPred3D is a new automated homology modeling program. Protein Structure Prediction
PockDrugPockDrug used physio-chemical and geometrical descriptors for finding pockets. Pocket Prediction
bSiteFinderMethod for identifying protein binding site. Binding site prediction
3DLigandSiteMethod for identifying ligand binding site. Binding site prediction
AutoSiteIn silico method for identifying small molecule binding site on receptor molecule. Binding site prediction
PocketDepthDepth based algorithm for identifying small molecule binding site. Binding site prediction
PocketAlignAlgorithm for comparing binding sites. Binding site comparison
LIGPLOTSoftware for plotting protein-small molecule interaction. Protein ligand interaction

Force field, molecular modeling, docking and Simulation related webservers

   Name of webservers                         Description   Category
CABS-FoldSimulation based molecular modeling webserver.Molecular modeling software
GalaxySiteWebserver utilizing docking for predicting binding site on protein. Binding site prediction
BSP-SLIMWebserver for low resoltuion docking using predicted structure. Docking software
PatchDockMethod for protein-protein, protein-small molecule docking. Docking software
SwissDockMethod for predicting protein-small molecule molecular interactions. Docking software
FireDockSoftware for refinement in molecular docking. Docking refinement software
DOCK-BlasterWebserver for structure based drug discovery using virtual screening. Virtual Screening
iScreenWebserver for virtual screening and de novo drug designing. Virtual Screening
DockingServerWebserver for protein-ligand docking. Docking software
Dock VisionComplete package consisting of all algorithms required for docking. Docking software
GFscoreScoring function for High throughput dockingScoring Function
Pose & RankWebserver for scorig of protein-ligand complexesScoring Function