Table 6.
Tools for predicting various sequence and structural features
| Name | Description | URL |
|---|---|---|
| 3dswap-pred | Classify a protein sequence as domain-swapping or non-domain swapping using an SVM model. | http://caps.ncbs.res.in/3dswap-pred/index.html |
| AAIndex | An amino acid index is a set of 20 numerical values representing various physico-chemical and biochemical properties of amino acids. | http://www.genome.jp/aaindex/ |
| Bioinformatics Link Directory (Protein) | Extensive list of tools for prediction of protein sequence features, structure features and function. | http://bioinformatics.ca /links_directory/category/protein |
| dbPTM | Comprehensive resource for protein PTMs. | http://dbptm.mbc.nctu.edu.tw/ |
| DISOPRED | Dynamically disordered protein chains do not have stable secondary structures and have high flexibility in solution. Disordered regions also play critical roles in protein function. | http://bioinf.cs.ucl.ac.uk/disopred/ |
| ELM | Eukaryotic Linear Motif server. | http://elm.eu.org/ |
| Eris | Eris server computes the change of the protein stability induced by mutations using structural data. | http://dokhlab.unc.edu/tools/eris/index.html |
| FoldAmyloid | Method for predicting of amyloidogenic regions from protein sequence. | http://bioinfo.protres.ru/fold-amyloid/oga.cgi |
| FoldX | FoldX can be used to find interactions contributing to the stability of proteins and protein complexes using structural data. | http://foldx.crg.es/ |
| Globplot | Globplot can predict disordered regions in protein sequence. | http://globplot.embl.de/ |
| H-Predictor | Predict hinge regions involved in protein oligomerization via the domain-swapping mechanism from structural data. | http://troll.med.unc.edu/dokhlab/index.php/Special:Hpredictor |
| Harmony | Substitution and propensity score-based protein structure assessment algorithm. | http://caps.ncbs.res.in/harmony/ |
| HORI | Webserver for prediction of higher order residue interactions in protein structures. | http://caps.ncbs.res.in/hori |
| InterPro | Integrated database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes. | http://www.ebi.ac.uk/interpro/ |
| IUPred | Prediction of intrinsically unstructured proteins. | http://iupred.enzim.hu/ |
| LIMBO | Predicts the amylogenic regions in a protein. | http://limbo.vib.be |
| MUPRO | Prediction of protein stability changes for single-site mutations from sequences. | http://mupro.proteomics.ics.uci.edu/ |
| NCBI-CDD | Extensive protein domain and family annotation database. | http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml |
| Pfam | Database of conserved protein domain families. | http://pfam.sanger.ac.uk/ |
| PFILT | Program to filter various sequence regions including low-complexity regions. | http://bioinfadmin.cs.ucl.ac.uk/downloads/pfilt/ |
| PIC | Protein interactions calculator. | http://pic.mbu.iisc.ernet.in/ |
| ProtParam | Compute biochemical features like Molecular Weight, Theoretical pI, Grand Average of Hydropathy (GRAVY), instability index, etc. | http://web.expasy.org/protparam/ |
| PSIPRED | Secondary structure prediction. | http://bioinf.cs.ucl.ac.uk/psipred/ |
| PURE | Prediction of unassigned regions in proteins. | http://caps.ncbs.res.in/pure |
| SABBLE | Relative solvent accessibility prediction. | http://sable.cchmc.org/ |
| ScanProsite | Report the functional motifs/patterns encoded in the sequence. Helps to assess the gain/loss of functional sites owing to mutation. | http://prosite.expasy.org/scanprosite/ |
| SignalP | Predicts the presence and location of signal peptide cleavage sites in amino-acid sequences. | http://www.cbs.dtu.dk/services/SignalP/ |
| SMART | Simple modular architecture research tool for assigning domains to protein. | http://smart.embl-heidelberg.de/ |
| TANGO | Predicts the aggregation-prone regions in a protein. | http://tango.crg.es/ |
| TargetP | Predicts the subcellular location of eukaryotic proteins. | http://www.cbs.dtu.dk/services/TargetP/ |
| UniProtKB | Catalog of information on proteins. | http://www.uniprot.org/ |
| WALTZ | Predicts the aggregation-prone regions in a protein. | http://waltz.vub.ac.be/ |