Title

A database for Plasmodium falciparum protein models

Authors

Ramasamy Gowthaman¹, Duraisamy Sekhar², Mridul Kumar Kalita¹ and Dinesh Gupta^1*

Affiliation

¹Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, INDIA; ²Current address: Dana-Farber Cancer Institute, Harvard Medical School, Dana-830, 44-Binney street, Boston, MA-02115, USA.

E-mail*

dinesh@icgeb.res.in; * Corresponding author

Phone

91 11 2617 3184

Fax

91 11 2616 2316

Article Type

Database

Date

received September 21, 2005; revised October 3, 2005; accepted October 3, 2005; published online October 5, 2005

Abstract

There is an urgent need for developing alternate strategies to combat Malaria caused by Plasmodium falciparum (P. falciparum) because of growing drug resistance and increased incidents of infection in humans. 3D models of P. falciparum annotated proteins using molecular modeling techniques will enhance our understanding about the mechanism of host parasite interactions for the identification of drug targets and malarial vaccine design. Potential structural templates for P. falciparum annotated proteins were selected from PDB (protein databank) using BLASTP (basic local alignment search tool for proteins). This exercise identified 476 Plasmodium proteins with one or more known structural templates (≥ 40% identity) for further modeling. The pair-wise sequence alignments generated for protein modeling were manually checked for error. The models were then constructed using MODELLER (a comparative protein modelling program for modelling protein structures) followed by energy minimization in AMBER force field and checked for error using PROCHEK.

Availability

http://bioinfo.icgeb.res.in/codes/model.html

Keywords

Molecular modeling; protein templates; comparative modeling; profile based alignment for modeling

Citation

Gowthaman et al., Bioinformation 1(2): 50-51 (2005)

Edited by

M. K. Sakharkar

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.