Table 1.
List of bioinformatics tools and databases used for sequence and structure-based function annotation
| S. no. | Name of Web server | URL | Uses | References |
|---|---|---|---|---|
| 1. Sequence similarity search tool | ||||
| BLAST: basic local alignment search tool | http://blast.ncbi.nlm.nih.gov/Blast.cgi | To find a similar sequence in the database | Mount (2007) | |
| 2. Biophysical and chemical characterization | ||||
| ProtParam | http://web.expasy.org/protparam/ | To calculate physical and chemical properties | Wilkins et al. (1999) | |
| 3. Sub-cellular localization of the protein | ||||
| I. | SOSUI | http://bp.nuap.nagoya-u.ac.jp/sosui/sosui_submit.html | To predict the transmembrane domain | Hirokawa et al. (1998) |
| II. | TMHMM | http://www.cbs.dtu.dk/services/TMHMM/ | Used to predict the transmembrane topology | Krogh et al. (2001), Sonnhammer et al. (1998) |
| III. | Psort II | http://psort.hgc.jp/form2.html | To predict sub-cellular localization | Nakai and Horton (1999) |
| IV. | SignalP | http://www.cbs.dtu.dk/services/SignalP/ | To predict cleavage site of signal protein | Petersen et al. (2011) |
| V. | HMMTOP | http://www.enzim.hu/hmmtop/index.php | To predict the transmembrane helix | Tusnady and Simon (2001) |
| 4. Functional analysis tool | ||||
| I. | Conserved domain | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi | To search conserved domain in the sequences | Marchler-Bauer et al. (2011) |
| II. | InterProScan | http://www.ebi.ac.uk/Tools/pfa/iprscan/ | To find the motif in the sequences | Quevillon et al. (2005) |
| III. | Interpro | http://www.ebi.ac.uk/interpro/ | To categorize by predicting domains and important sites | Apweiler et al. (2001) |
| IV. | SMART | http://smart.embl-heidelberg.de/ | To Identify and annotate domains in protein | Letunic et al. (2012) |
| V. | CATH | http://www.cathdb.info | To use hierarchical domain classification of PDB structures | Orengo et al. (1997) |
| VI. | Pfam | http://pfam.sanger.ac.uk | To collect protein families, based on multiple sequence alignments and HMM | Finn et al. (2014) |
| 5. Predicting the fold pattern | ||||
| I. | PFP-FunDSeqE | http://www.csbio.sjtu.edu.cn/bioinf/PFP-FunDSeqE/ | To find the type of protein fold in the protein sequences | Shen and Chou (2009) |
| II. | HHpred | http://toolkit.tuebingen.mpg.de/hhpred | Used for homology detection | Kalev and Habeck (2011) |
| III. | Dali server | http://ekhidna.biocenter.helsinki.fi/dali_server/start | For searching similar 3D structure | Holm and Rosenstrom (2010) |
| 6. Virulence prediction | ||||
| FungalRV | fungalrv.igib.res.in/query.php | In adhesin prediction | Chaudhuri et al. (2011) | |
| 7. Structure prediction | ||||
| I. | MODELLER | http://salilab.org/modeller/ | To model three-dimensional structures | Webb and Sali (2014) |
| II. | SWISS-MODEL | http://swissmodel.expasy.org/ | Homology modeling server | Biasini et al. (2014) |
| III. | Phyre2 | www.sbg.bio.ic.ac.uk/phyre2 | Ab initio method for structure prediction | Kelley and Sternberg (2009) |
| 9. Structure validation | ||||
| SAVES | http://autodock.scripps.edu/ | To validate protein structures | Laskowski et al. (1996) | |
| 10. Docking analysis | ||||
| AutoDock | http://autodock.scripps.edu/ | Sandeep et al. (2011) | ||