How to write a project on BioinformaticsProject title: Biomedical informatics Centre of

Principal Investigator

Co-PI (name & address): -

Date of start:

Duration: 3 years

Objectives of the proposal:

a) Drug Discovery: To use the tools available for the design and development of lead molecules.

b) Database Development: To develop and support databases of proteins related to diseases

c) To identify, analyse and model the proteins differentially expressed in patients suffering from neurological disorders in an effort to develop a biomarker for the identification of the disease.

d) To increase the understanding in the use of tools in bioinformatics and modern biology via workshops and training programs

Methodology:

The Discovery Studio and GCG softwares which have been provided as part of the centre are being extensively used in the research work. In addition to this other bioinformatics tools which are being used to promote research include:

a) FASTA, BLAST, CLUSTALW, and InterPro: The protein and DNA sequence analyses were performed by using these online softwares b) In addition to using Discovery Studio, a number of other online softwares used for the tertiary and secondary structure prediction of proteins. Docking studies were also carried out using these softwares. These softwares include PsiPred, SWISS-PROT, AUTODOCK 3

Interim modification of objectives/

Methodology (with justifications): Nil

Summary on progress (during the period of report):

In addition to Accelrys Discovery Studio and GCG provided, a number of free softwares have also installed for the use in the centre. These include:

1. AutoDock and FTDock for molecular modeling and docking

2. GROM The following work was undertaken during the first year of the project.ACS for molecular simulations

3. PyMOL and Swiss-PDBviewer for Molecular visualization

4. PHYLIP and MEGA for analysis and inference of phylogenetic trees and evolution

5. MySQL/PHP for development of databases

6. MODELLER for homology modeling

A) Initiated research projects Project No.

Name

A. In-house Projects 1. In silico design of small peptide inhibitors for novel

targets of Mycobacterium tuberculosis (M.tb) Targets:

Dihydrodipicolinate Reductase (Dhpr): Shikimate Kinase: Thymidylate Synthase (Ts): Thymidylate Kinase (Tmpkmtb)

2. In Silico Design of Small Peptide Inhibitors for Novel Drug Targets for Cancer

3. Development of Databases for Cancer4. Dbmdbase: Development of Databases for Type 2

Diabetes Mellitus 5. Development of Databases for Cancer related protein.

B. Projects for other Investigators 6. Development of a Clinical Patient Record System for

Rural Cancer 7. Homology Modeling of apical membrane antigen1

(PvAMA) from Plasmodium vivax and identification of polymorphic sites

8. Homology Modeling of Plasmodium vivax Dihydrotperoate Synthase: Novel Single mutant and triple mutants and analysis of sulfadoxine resistance.

9. Pattern Identification of HupB protein of MTb.