| Name of webservers | Description | Category | |
| WHAT IF | This server find structural problems in PDB entries that have been determined using X-ray diffraction or NMR techniques. | Protein verification tool |
| pdb-care | It aids experimentalists in detecting discrepancies in connectivities and nomenclature. | Detect error in PDB entries. |
| CPHModels | This method is homology modeling software and is based on profile alignment guided by secondary structure and exposure prediction. | Protein structure prediction |
| SWISS-MODEL | This method is a fully automated homology modeling server used for iprotein structure prediction. | Protein structure prediction |
| WHAT_CHECK | It is a refinement tool for PDB, it finds incorrect structure. | Protein verification tool |
| 3vee | 3vee is collection of program for the assessment of volumes in protein files. | Protein Volume assessment |
| 3DLigandSite | 3DLigandSite is an automated method for the prediction of ligand binding sites. | Protein binding site prediction |
| IntFOLD | The 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 |
| firestar | firestar server: predicting functional residues from structural templates and alignment reliability. | Prediction of functional residues |
| SA-Mot | It extract structural motifs from protein loop structures using HMM-SA. | Extract structural motifs |
| CSpritz | CSpritz server predict Disorder region in proteins. | Protein disorder prediction |
| NetTurnP 1.0 | NetTurnP server predict Beta-turn regions in protein sequences. | Protein structure prediction |
| NetSurfP ver. 1.1 | NetSurfP ver. 1.1 - Protein Surface Accessibility and Secondary Structure Predictions. | Protein structure prediction |
| SCRATCH | Protein structure prediction including various related servers. | Protein structure prediction |
| BETApro | The Server of Predicting Beta-Residue Pair, Strand Pair, Strand Alignment, and Beta-Sheet Architecture. | Protein structure prediction |
| TMBpro | Transmembrane Beta-Barrel Secondary Structure, Beta-Contact, and Tertiary Structure Predictor. | Protein structure prediction |
| SIDEpro | SIDEpro is a novel machine learning approach for the fast and accurate prediction of side-chain conformations. | Protein structure prediction |
| APSSP2 | This 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 |
| PROTEUS2 | PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. | Protein Structure prediction |
| BetaTPred3 | The server is developed for predicting beta turns based on propensity score. | Protein Structure Prediction |
| BetaTurns | Betaturns 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 |
| PORTER | Porter: a new, accurate server for protein secondary structure prediction. | Protein secondary structure prediction |
| PPCpred | This server is designed for sequence-based prediction of protein crystallization, purification, and production propensity. | prediction of Protein crystallization |
| YASPIN | A simple and fast secondary structure prediction method using hidden neural networks. | Protein secondary structure prediction |
| SARpred | SARpred is a ANN based computational method for predicting protein surface accessibility. | Prediction of surface accessibility |
| SANN | SANN is nearest neighbor based method developed for predicting protein surface accessibility. | Prediction of surface accessibility |
| PSIPRED | Server utilizes evolutionary information in form of alignment profile for structure prediction | Protein secondary structure prediction |
| SOPMA | Method is based on protein family alignment profile for structure prediction | Protein secondary structure prediction |
| AlphaPred | The AlphaPred server predicts the alpha turn residues in the protein sequence. | Protein Structure Prediction |
| HSPred | HSPred 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 |
| GammaPred | The GammaPred server predicts the gamma turn residues in the protein sequence. | Protein Structure Prediction |
| BhairPred | BhairPred 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 |
| Multicoil | The MultiCoil program predicts the location of coiled-coil regions in amino acid sequences and classifies the predictions as dimeric or trimeric. | Primary structure analysis |
| CFSSP | This server predicts secondary structure of protein from the amino acid sequence. | Secondary structure prediction |
| PREDATOR | Method based on hydrogen bonded residues in a single amino acid sequence | Protein secondary structure prediction |
| Jpred4 | A consensus method for protein secondary structure prediction at University of Dundee | Secondary structure prediction |
| STRAP | The free computer program STRAP aligns proteins by sequence and 3D-structure. | Tertiary structure analysis |
| TopMatch-web | Protein structure comparison | Tertiary structure analysis |
| 3Djigsaw | Three-dimensional models for proteins based on homologues of known structure | Tertiary structure prediction |
| Geno3d | Automatic modelling of protein three-dimensional structure | Tertiary structure prediction |
| Phyre2 | Automated 3D model building using profile-profile matching and secondary structure | Protein structure prediction |
| ITASSER | Software for protein structure prediction using threading approach | Protein structure prediction |
| ROBETTA | Comparative and de novo approcah based structure prediction software | Protein structure prediction |
| QUARK | Ab inition based protein folding and structure prediction software | Protein folding and structure prediction |
| Bhageerath-H | Homology and ab initio approcah based structure prediction software | Protein structure prediction |
| MODELLER | Homology and comparative modeling based approcah for structure prediction | Protein structure prediction |
| GalaxyWEB | Suite for protein structure prediction, refinement and interaction software | Protein structure prediction, refinement and interaction |
| SCRATCH | Complete package for protein analysis | Protein structure analysis |
| MULTICOM | Method utilizes information from multiple sources for building models | Protein structure prediction |
| ModWeb | Template based structure prediction software | Protein structure prediction |
| PS2 | Protein structure prediction software which uses comparative modeling approach | Protein structure prediction |
| RaptorX | Nonlinear scoring function for predicting structure of non-homologous proteins | Protein structure prediction |
| HMMSTR/Rosetta | Prediction of protein structure from sequence | Tertiary structure prediction |
| EDS | The 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 |
| FATCAT | Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) is a flexible protein structure comparison algorithm. | Structure Alignment and Comparison |
| QMEANclust | QMEANclust perform estimation of protein model quality by combining a composite scoring function with structural density information. | Protein Structure Quality Assessment |
| Pcons | Pcons is a Protein Structure Prediction Meta Server. | Protein Structure Prediction |
| ModFOLDclust | This 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-WQA | It is method for quality assessment in protein structure prediction. | Protein Structure Quality Assessment |
| ESyPred3D | ESyPred3D is a new automated homology modeling program. | Protein Structure Prediction |
| PockDrug | PockDrug used physio-chemical and geometrical descriptors for finding pockets. | Pocket Prediction |
| bSiteFinder | Method for identifying protein binding site. | Binding site prediction |
| 3DLigandSite | Method for identifying ligand binding site. | Binding site prediction |
| AutoSite | In silico method for identifying small molecule binding site on receptor molecule. | Binding site prediction |
| PocketDepth | Depth based algorithm for identifying small molecule binding site. | Binding site prediction |
| PocketAlign | Algorithm for comparing binding sites. | Binding site comparison |
| LIGPLOT | Software for plotting protein-small molecule interaction. | Protein ligand interaction |