How to write a project on Bioinformatics

Project 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 Name

Project No.
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 Cancer
4. 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.