Table 1.
Common methods to characterize proteins and the main evolutionary pattern they rely on (See text for citations)
| Method | Website | Comments |
|---|---|---|
| Gene Ontology | http://www.geneontology.org | Standard representation of gene and gene product attributes |
| Enzyme Nomenclature | http://www.chem.qmul.ac.uk/iubmb/enzyme | Enzyme classification |
| BLAST/PSI-BLAST | http://blast.ncbi.nlm.nih.gov/Blast.cgi | Sequence comparison |
| Gotcha | http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html | Assigns GO terms based on sequence comparison |
| ESG | http://kiharalab.org/web/esg.php | Assigns GO terms based on sequence comparison |
| GOPred | http://kinaz.fen.bilkent.edu.tr/gopred | Assigns GO terms based on sequence comparison |
| Pfam | http://pfam.sanger.ac.uk | Database of protein families and their MSA |
| HMMER | http://hmmer.janelia.org | Sequence comparison based on hidden markov models |
| Prosite | http://prosite.expasy.org | Database of protein domains, families and functional sites |
| Interpro | http://www.ebi.ac.uk/interpro | Database of protein functional signatures |
| ELM | http://elm.eu.org/links.html | Resource to investigate functional sites in eukaryotic proteins |
| ConFunc | http://www.sbg.bio.ic.ac.uk/~confunc | Assigns GO terms based on sequence comparison |
| DME | http://adios.tau.ac.il/DME11.html | Assigns full EC number based on sequence comparison |
| Eficaz2 | http://cssb.biology.gatech.edu/skolnick/webservice/EFICAz2/index.html | Assigns full EC number based on sequence comparison |
| Dali | http://ekhidna.biocenter.helsinki.fi/dali_server | 3D protein structure comparison |
| TM-align | http://zhanglab.ccmb.med.umich.edu/TM-align | 3D protein structure comparison |
| TOPS++FATCAT | http://fatcat.burnham.org/TOPS | 3D protein structure comparison |
| CATH | http://www.cathdb.info | Protein domain structure classification |
| SCOP | http://scop.mrc-lmb.cam.ac.uk/scop | Protein domain structure classification |
| ConCavity | http://compbio.cs.princeton.edu/concavity | Predicts ligand binding sites from protein structure |
| FTSite | http://ftsite.bu.edu | Predicts ligand binding sites from protein structure |
| LIGSITEcsc | http://projects.biotec.tu-dresden.de/pocket | Predicts ligand binding sites from protein structure |
| 3DLigandSite | http://www.sbg.bio.ic.ac.uk/~3dligandsite/ | A threading-based method to predict ligand binding site |
| FINDSITE | http://cssb.biology.gatech.edu/skolnick/files/FINDSITE | A threading-based method to predict binding site, ligand, and function |
| pevoSOAR | http://sts.bioengr.uic.edu/pevosoar | Assigns up to four digit EC numbers based on local structure similarities |
| Catalytic Site Atlas | http://www.ebi.ac.uk/thornton-srv/databases/CSA | Database of known and predicted catalytic residues in the protein structures |
| FunClust | http://pdbfun.uniroma2.it/funclust | Identifies local functional motifs in the protein structures |
| GASPSdb | http://gaspsdb.rbvi.ucsf.edu | Database of 3D motifs generated by GASPS algorithm |
| SuMo | http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome | 3D structure comparison based on local structure similarity |
| Par-3D | http://sunserver.cdfd.org.in:8080/protease/PAR_3D/index.html | Detects active site residues using 3D templates |
| PINTS | http://www.russelllab.org/cgi-bin/tools/pints.pl | 3D structure comparison based on non-sequential local motifs |
| Flora | http://www.mcsg.anl.gov/ | Assigns three digit EC numbers based on local structural similarities |
| GeMMA | http://www.biochem.ucl.ac.uk/cgi-bin/dlee/GeMMA | Provides classification based on phylogenetic analysis |
| SCI-PHY | http://phylogenomics.berkeley.edu/ | Provides classification based on phylogenetic analysis |
| PROTONET | http://www.protonet.cs.huji.ac.il | Classifies protein sequences based on phylogenetic analysis |
| SIFTER | http://sifter.berkeley.edu | Assigns GO terms based on phylogenetic analysis |
| PhylomeDB | http://phylomedb.org/ | Database of phylogenetic trees with ortholog assignments |
| TreeFam | http://www.treefam.org/ | Database of phylogenetic trees with ortholog assignments |
| ET | http://mammoth.bcm.tmc.edu/ETserver.html | Ranks amino acids based on phylgenetic analysis |
| ETA | http://mammoth.bcm.tmc.edu/eta | Assigns three digit EC numbers and GO terms based on local structural similarities |