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| Purpose | Name | URL | Description and advantages/disadvantages |
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| Databases | OMIM | http://www.ncbi.nlm.nih.gov/omim | Manually curated, freely available |
| dbSNP | http://www.ncbi.nlm.nih.gov/SNP/ | Freely available. Includes short variations in nucleotide sequences from a wide range of organisms |
| 1000 Genomes: A Deep Catalog of Human Genetic Variation | http://www.1000genomes.org/ | Freely available, provides tools for various searches as within populations, allele frequency and linkage disequilibrium structure |
| HGMD | http://www.hgmd.org/ | Requires license, but is the most comprehensive database of human mutations and provides visualization tools and search engines |
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| Networking | Cytoscape | http://www.cytoscape.org/ | An open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles, and other state data |
| Network Portal | http://networks.systemsbiology.net/ | Provides analysis and visualization tools for selected gene regulatory networks to aid researchers in biological discovery and hypothesis development |
| Network2Canvas | http://www.maayanlab.net/N2C/#.U1fP4qJWAkI | Allows for generation of drug-drug similarity and functional association of gene canvases |
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| 3D structure modeling | Swiss Model | http://swissmodel.expasy.org/ | Automated server allowing 3D structure of a protein to be predicted inputting the sequence of the target |
| I-TASSER | http://zhanglab.ccmb.med.umich.edu/I-TASSER/ | Fully automated 3D structure predictor, especially useful for difficult targets (low sequence similarity to known structures) |
| Modeller | http://salilab.org/modeller/ | Stand-alone 3D structure predictor. Can be installed locally and used for large-scale predictions |
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| Protein stability | FoldX | http://foldx.crg.es/ | Fast assessment of the changes of the unfolding free energy caused by mutations using empirical formula |
| I-Mutant | http://gpcr2.biocomp.unibo.it/%7Eemidio/I-Mutant/I-Mutant.htm | Very fast and accurate prediction of the changes of the folding free energy caused by mutations. The input can be just the sequence of the protein |
| ERIS | http://dokhlab.unc.edu/tools/eris/ | Uses Medusa force field to make predictions of the change of the folding free energy caused by mutations |
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| Protein interactions | BeAtMuSiC | http://babylone.ulb.ac.be/beatmusic/ | Evaluates change in binding affinity between proteins caused by single-site mutations in their sequence |
| ICM | http://www.molsoft.com/gui/mutation-protein-binding.html | Computes the change in binding free energy of a protein complex upon mutation of a single residue. Requires license |
| Robetta | http://robetta.bakerlab.org/alascansubmit.jsp | Provides estimation for the binding free energy changes caused by mutations to Alanine |
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| Subcellular localization and pH dependence | WoLF PSORT | http://wolfpsort.org/ | Predicts the subcellular localization of proteins based on their amino acid sequences. The predictions are based on both known sorting signal motifs and amino acid content |
| PredSL | http://aias.biol.uoa.gr/PredSL/ | Stand-alone code utilizing neural networks, Markov chains, and HMMs for the prediction of the subcellular localization of proteins |
| UniLoc | | This is a webserver using PSI-Blast to infer homology between query sequence and already annotated proteins |
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| Macromolecular function | SNAP | https://www.rostlab.org/services/snap/ | SNAP is a neural network-based method that uses in silico derived protein information (e.g., secondary structure, conservation, solvent accessibility, etc.) in order to make predictions regarding functionality of mutated proteins |
| MutationAssessor | http://mutationassessor.org/ | The server predicts the functional impact of amino acid substitutions in proteins |
| SIFT | http://sift.jcvi.org/ | The prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences |
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