| BindUP | Prediction of DNA and RNA binding proteins |
| CASTp | Computed atlas of surface topography of proteins. |
| Consurf Server | Server for the identification of functional regions in proteins. |
| DynDom | DynDom is a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available. |
| GCUA - Graphical Codon Usage Analyser | Usage of each codon in the sequence will be plotted against the fraction of usage of the codon in the selected organism. |
| GRASP-suite | GRASP-suite is a collection of tools and tutorials to perform and analyse ancestral sequence reconstruction. |
| GalaxyWEB | A web server for protein structure prediction, refinement, and related methods. |
| I-TASSER | Iterative Threading ASSEmbly Refinement is a hierarchical approach to protein structure and function prediction. |
| IUPred | IUPred3 is a combined web interface that allows to identify disordered protein regions using IUPred2 and disordered binding regions using ANCHOR2. |
| Mol* (/'molstar/) | Web-based open-source toolkit for visualisation and analysis of large-scale molecular data |
| Motif Scan | Searches for all known motifs that occur in a sequence. |
| Multiple Sequence Alignment (MSA) Clustal Omega | Multiple Sequence Alignment for DNA or proteins. |
| NetOGlyc | Neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. |
| PI2PE | Protein Interface/Interface Prediction Engine |
| PROMPT | Compare protein sets for features like molecular weight, isoelectric point, enzyme classifications or structural classes. |
| PROVEAN | Protein Variation Effect Analyzer - A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. |
| PSIPRED | Protein Sequence Analysis Workbench of secondary structure prediction methods. |
| Phyre2 | Protein Homology/analogY Recognition Engine - Protein structure prediction |
| PolyPhen-2 | Polymorphism Phenotyping tool that predicts possible impact of an amino acid substitution on the structure and function of a human protein. |
| ProSA-web | Interactive web service for the recognition of errors in three-dimensional structures of proteins. |
| ProtParam | Calculates amino acid composition, theoretical pI, molecular weight. |
| Protein Digest | For a given protein sequence presents lists of peptides that would be produced using Trypsin, chymotrypsin, elastase, cyanogen bromide, iodosobenzoate etc. |
| 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. |
| ncoils | Program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. |
