About the Bioinformatics Centre

The Bioinformatics Infrastructure Facility (BIF) at Jamia Hamdard (JH) was created in 2008-09 under the BTBI program of DBT with a mandate of supporting bioinformatics teaching and research at JH.


Area of Specialization: BIF JH is emerging as one of the potential centers of education and research in bioinformatics, particularly in the area of drug design and development.

The mandate of the center is to carry out and promote research in the area of drug designing and development, computational biology, and systems biology.
Current area of research

Currently, the focus of research is the application of computational design of some novel, non-pteridine analogs as selective Mycobacterium tuberculosis dihydrofolate reductase (MtbDHFR) inhibitors. Recently BIF JH has been sanctioned a project by DBT. The project, Computational Design of Some Novel, Non-pteridine Analogs as Selective Mycobacterium tuberculosis Dihydrofolate Reductase Inhibitors, relates to the development of selective MtbDHFR inhibitors through in silico and experimental approaches. In this project, a selective test ligand – designed and synthesized in our chemistry lab – is being investigated as a potent non-pteridine analog

Superimposed methotrexate (green) and theest ligand.
The center adopts a multi-criteria drug design approach which, as opposed to earlier approach to drug discovery - which focuses on the activity first and then address other issues related to ADMET - deals with the simultaneous handling of multiple properties of interest, including the medicinal chemistry and biochemistry, and represents a necessary shift of paradigm from sequential to multi-criteria drug discovery. This approach of drug discovery involves utilization of in silico tools for multi-objective optimization, typically using all available computer models and checking a few of the most critical criteria experimentally.

The BIF JH is consistently mentoring students in project/dissertation work, and has provided training to postgraduate students on topics such as the in silico structure assessment analysis of core domain of four protein data bank entries of HIV-1 protease, in silico inhibitor identification from natural compounds for acetylcholine esterase, in silico approach to arsenic bioremediation, and 3D QSAR and pharmacophore design and drug target validation and prioritization, besides holding hands-on training and seminars/workshops each year since its inception. The centre has organized workshops on application of bioinformatics in drug discovery and development, computer aided drug design, chemo-bioinformatics and computational biology, and multicriteria drug design.

In future, BIF JH shall continue its ongoing work on the application of computational techniques for designing and development of new drugs, particularly the target-based drug designing, 3D QSAR and pharmacophore design, and drug target validation and prioritization, besides augmenting research in the area of computational and systems biology and molecular interactions.

Inter Institutional collaboration

JH has entered into an agreement (MoA) to carry out research with institutes like IIIM Jammu, ICGEB and URDIP (CSIR). In 2013, one of the students under this category completed his PhD thesis work on Structure Prediction and Molecular Modeling Analysis of Therapeutically Important Targets using in silico Approach and was awarded PhD in Bioinformatics from JH. More students are working for their doctoral research on In silico Approach to Study Novel Anticoagulants, and Rational Inhibitor Design and Iterative Screening for Potential Anti-carcinogenic Agents. As part of the collaborative research with ICGEB, BIF JH has recently got a student enrolled for PhD at JH to work on computational prediction of gene regulatory networks using gene sequence and expression data.

Infrastructure facilities
BIF JH is equipped with Database/Application Server and a medium end (Proxy & File) server and desktops (11) with OS and the following licensed software for molecular modeling and drug design, especially for molecule draw, visualization and analysis (vLifeBase), all molecular operations and key activity of conformer generation (vLifeBase), homology modeling with options for manual and automated template based modeling (ProModel), docking studies with multiple scoring functions and options for rapid and high precision docking (vLifeDock), 2D/3D QSAR with multiple variable selection options and regression methods (vLifeQSAR), exploring databases with multiple search options including property, fingerprint and pharmacophore (ChemDBS), pharmacophore generation and application in optimization and searches (MolSign), creating combinatorial library with a choice of substitutions (LeadGrow), calculating and visualizing molecular properties on the surface of a molecule (ProViz), and molecular modeling and simulation by tripose (SYBYL-X Suite). Bioinformatics lab is equipped with an overhead projector and an interactive board to facilitate the training of students.

About the Institution

Jamia Hamdard is a Health Science University. It got the deemed to be University status by the HRD Ministry in 1989. Over the years, Jamia Hamdard has emerged as an outstanding institution of higher learning with distinct and focused academic programs in Medical Sciences, Pharmacy and Basic Sciences, and allied disciplines including the Nursing, Physiotherapy and Occupational Therapy, besides contributing to higher education in Information Technology, Computer Applications and Management. Jamia Hamdard is known for its programs both in India and abroad. The various faculties and departments of the University are equipped with state-of-the-art facilities for research and publish hundreds of papers every year in peer reviewed journals of international repute. Research projects worth millions of rupees have been sanctioned and completed by the faculty of the University. The University has been accredited two times in ‘A’ category by NAAC. .

Achievements at a glance

BIF JH has engaged itself in research on various areas in bioinformatics, and within the last few years since its inception, has worked on pharmacophore model generation and 3D quantitative structure-activity relationship (QSAR) analysis of N-acyl and N-aroylpyrazolines for enzymatic and cellular B-Raf kinase inhibition, 3D-QSAR for quinoline, benzimidazole and benzofuran-based analogs as phosphodiesterases IV (PDE-IV) inhibitors, and also on amino-substituted pyrido[3,2B]pyrazinones as PDE-5 inhibitors, besides working on the basic science subjects such as the distribution of amino acid in non-membrane protein in prokaryotic and eukaryotic system, and prediction of protein tertiary structure of novel peptides isolated from scorpion venom. In the studies of venom peptides, two novel peptides have been isolated and their structure was predicted using prediction software (Fig. 1).

Tertiary structure of novel peptides - (a) a 4.237 kDa (69 residues) and (b) a 16.39 kDa (93 residues) peptide - isolated from scorpion venom. The amino acid sequence of peptides was determined by MALDI-TOF/MS, and the tertiary structure was deduced and validated using protein tertiary structure prediction software. The peptides have been found to induce apoptosis in neuroblastoma and breast cancer cell lines.
Recent publications


Akranth Marella et al (2013) 3D Quantitative structure-activity relationship for quinoline, benzimidazole and benzofuran-based analogs as phosphodiesterases IV (PDE-IV) inhibitors, Medicinal Chemistry Research, DOI 10.1007/s00044-012-0457-4

Omprakash Tanwar et al (2012) Pharmacophore model generation and 3D-QSAR analysis of N-acyl and N-aroylpyrazolines for enzymatic and cellular B-Raf kinase inhibition, Medicinal Chemistry Research, DOI 10.1007/s00044-012-0210-z

Omprakash Tanwar et al (2012) 3D-QSAR of amino-substituted pyrido[3,2B]pyrazinones as PDE-5 inhibitors, Medicinal Chemistry Research, 21:202–211 

RK Gaur (2009) Prokaryotic and eukaryotic non-membrane proteins have biased amino acid distribution, Journal of Computer Science and Systems Biology 2(6), 298-299 

Faculty members



Prof. Shakir Ali,

Coordinator, BIF Jamia Hamdard University, New Delhi

Dr. Mymoona Akhtar

, Dyputy Coordinator, BIF Jamia Hamdard, New Delhi




Prof. Shakir Ali
Head, Department of Biochemistry
Faculty of Science, Jamia Hamdard
Hamdard Nagar, New Delhi 110062

Dy. Coordinator:

Dr. Mymoona Akhter
 Assistant Professor, Department of Pharmaceutical Chemistry
Faculty of Pharmacy, Jamia Hamdard
Hamdard Nagar, New Delhi 110062

Phone Number

091(11)26059688 (Extn. 5510)




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