| Online Tool | Description |
|---|
| Block Maker | Finds conserved blocks in a group of two or more unaligned protein sequences. |
| CASTp | Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. |
| ClustalW2 | Multiple Sequence Alignment for DNA or proteins |
| ExPASy Proteomics Tools | Diverse utilities for protein identification and characterization. |
| GRAMM-X Protein-Protein Docking Web Server | Provides predicted PDB models for docking of two proteins. |
| Ligand-Protein Contacts (LPC) | Analysis of inter-atomic contacts in ligand-protein complexes, and inter-atomic contacts in protein entries. |
| MolAxis | Identification of channels in macromolecules. |
| Motif Scan | Searches for all known motifs that occur in a sequence. |
| NetOGlyc | Neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. |
| Patch Finder | Find and display the largest positive electrostatic patch on a protein surface. |
| PDB Goodies | Input PDB file. Output includes amino acid composition, molecular weight, volume, bond lengths, bond angles, and torsion angles. Change the residues to poly-Ala. Remove HETATM(s) present in the PDB file. |
| Phyre2 | Protein Homology/analogY Recognition Engine - Protein structure prediction |
| PI2PE | Protein Interface/Interface Prediction Engine |
| PoreWalker | Detection and characterisation of transmembrane protein channels from their 3D structure. |
| ProFace | Analysis of Protein-Protein Interface |
| PROMPT | Compare protein sets for features like molecular weight, isoelectric point, enzyme classifications or structural classes. |
| Protein Digest | For a given protein sequence presents lists of peptides that would be produced using Trypsin, chymotrypsin, elastase, cyanogen bromide, iodosobenzoate etc. |
| Protein-Protein Interaction Server | Online tool to analyze the protein-protein interface of any protein complex. |
| ProtParam | Calculates amino acid composition, theoretical pI, molecular weight. |
| PSA Protein Structure Prediction Server | Prediction of secondary structures and folding classes for a given amino acid sequence. |
| PSORT | Prediction of protein sorting signals and localization sites. |
| QuasiMotiFinder | A server for the identification of signatures and signature-like patterns in protein sequences. |
| SignalP | Server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. |
| SWISS-MODEL | An Automated Comparative Protein Modeling Server |
| TM-align | Structural alignment program for comparing two proteins. |
| VADAR | VADAR (Volume, Area, Dihedral Angle Reporter) is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data. |
