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Web Servers

This site maintain links of web servers which provides online service for predicting structure and function of proteins at residue level.

   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.
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
BetaTPredThe server BetaTPred is developed for predicting ß-turns in a protein from the amino acid sequence.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
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
TMBETA-NETTMBETA-NET: Discrimination and Prediction of Transmembrane Beta Strands in Outer Membrane Proteins from amino acid sequence. Prediction of Transmembrane Beta Strands
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
Protein Colourer It is a tool for coloring your amino acid sequencePrimary structure analysis
CFSSPThis server predicts secondary structure of protein from the amino acid sequence.Secondary structure prediction
JpredA consensus method for protein secondary structure prediction at University of DundeeSecondary structure prediction
MolTalkMolTalk is a computational environment for doing Structural Bioinformatics. It interprets PDB formatted files and creates an object representation of the structure-chain-residue-atom hierarchy.Tertiary structure analysis
Seq2StructSeq2Struct, a web resource for the identification of sequence-structure links.Tertiary structure analysis
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
PhyreAutomated 3D model building using profile-profile matching and secondary structureTertiary structure prediction
HMMSTR/Rosetta Prediction of protein structure from sequenceTertiary structure prediction
CASTp It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other moleculesSurface topology of proteins
TOPSANThe TOPSAN project was developed to collect, share, and distribute information about protein three-dimensional structures.Protein 3D structures analysis
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.CASP winner
PconsPcons is a Protein Structure Prediction Meta Server.CASP winner
ModFOLDclustThis server for predicting the quality of three-dimensional (3D) models is fundamentally important for the success of tertiary structure (TS) prediction strategies.CASP winner
ProQProQ - is a neural network based predictor that based on a number of structural features predicts the quality of a protein model.CASP winner
MUFOLD-WQAIt is method for quality assessment in protein structure prediction.CASP winner
MUFOLD-QAIt is method for quality assessment in protein structure prediction.CASP winner
ESyPred3DESyPred3D is a new automated homology modeling program. Homology modeling server