Title

ContPro: A web tool for calculating amino acid contact distances in protein from 3D -structures at different distance threshold

Authors

Ahmad Firoz1*, Adeel Malik¹, Obaid Afzal², Vivekanand Jha^{1, 3}*

Affiliation

¹Biomedical Informatics Center, PGIMER, Chandigarh, India; ²Faculty of Pharmacy, Jamia Hamdard, New Delhi, India; ³Department of Nephrology, PGIMER, Chandigarh, India

E-mail*

firoz@bmi.icmr.org.in; * Corresponding author

Article Type

Database

Date

received  May8, 2010; accepted  June8, 2010; published online July6, 2010

To investigate the functional sites on a protein and the prediction of binding sites (residues) in proteins, it is often required to identify the binding site residues at different distance threshold from protein three dimensional (3D) structures. For the study of a particular protein chain and its interaction with the ligand in complex form, researchers have to parse the output of different available tools or databases for finding binding-site residues. Here we have developed a tool for calculating amino acid contact distances in proteins at different distance threshold from the 3D-structure of the protein. For an input of protein 3D-structure, ContPro can quickly find all binding-site residues in the protein by calculating distances and also allows researchers to select the different distance threshold, protein chain and ligand of interest. Additionally, it can also parse the protein model (in case of multi model protein coordinate file) and the sequence of selected protein chain in Fasta format from the input 3D-structure. The developed tool will be useful for the identification and analysis of binding sites of proteins from 3D-structure at different distance thresholds.

Availability

Citation

Firoz et al. Bioinformation 5(2) 55-57 (2010)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.