Knowledge Discovery in Life Sciences:
Modeling of Small Molecules to Macromolecules

December 11 – December 17 2007
Bioinformatics Centre
University of Pune
Pune 411 007

Bioinformatics Centre, University of Pune
Bioinformatics centre, established in 1987, is actively pursuing research in the field of Bioinformatics and Chemoinformatics with an aim to integrate the knowledge extracted from biological and chemical space. The bioinformatics research in this centre primarily focuses on structure-based (molecular modeling, prediction of 3D structures of biological macromolecules, force field development), sequence-based (Comparative Genomics), Systems (Metabolic pathways analysis and Modeling) and quantum (DFT, QM/MM) chemistry approaches. The Chemoinformatics research has main emphasis on structure/ligand based virtual screening, scoring function development using fuzzy logic, and lead optimization. Apart from aforementioned, the centre also pursues active research in web-server (CEP) and database development both in the field of biology (Virgen) and chemistry (Tbdb).
    The centre has been recognized as “centre of excellence” for research and human resource development in the field of bioinformatics by Government of India (Department of Biotechnology and Ministry of Communication and Information Technology). The centre, over the years, has organized various international conferences and workshops in field of bioinformatics.  Under the auspices of Department of Biotechnology, Govt. of India, the centre is coordinating (and jointly conducting) the national Bioinformatics Certification Examination (BINC) since 2005.

Under the leadership of Prof. G.N.Ramachandran and his group at Chennai and Bangalore has established the importance of theoretical study on Biomolecular structure and functional relationship. Availability of high resolution X-ray and NMR structures and the genome sequences has provided us with a data rich environment to analyze the interaction between the biomolecules to explain their functional role in biology. The data generated at various levels of biocomplexity provided scientific community with an unlimited opportunity for data mining and knowledge discovery. Concurrent to these developments, one can sense, a growing inclination towards the paradigm of rational approach of drug/lead discovery. Thus, to make most from the development of genomics and proteomics, alongside that from the data describing the modulation of genes and proteins via diverse libraries of small molecules; a pressing need to develop a 'chemistry-aware' biology interface is felt. Such integration can lead us towards better and holistic understanding of the complexity of biological/chemical phenomena associated with diseases. The over-whelming response of participants of our previous workshops has helped us to identify and plan yet another unique theme. The proposed workshop aims at providing training of the-state-of-the-art tools and techniques in Bioinformatics and Chemoinformatics.

Understanding and characterisation of the phenomenon of the molecular association like DNA-Protein, Protein-Carbohydrate and receptor-ligand complex formation is one of the important steps in any successful rational drug discovery process. The use of computational tools and algorithms can facilitate knowledge extraction from the structural aspect of the macromolecules. Alongside the importance of protein in biological interaction, this workshop will equally emphasize on the structure of DNA, RNA and Carbohydrate, considering the emerging importance of Glyco-biology, Transcription factor and anti-sense RNA. This can help us understanding the critical conformational changes underlines the biological functioning on macroscale.
The importance of shape and electrostatics as primary variables for describing the chemistry of molecular interactions will be emphasized alongside a preference for the rigorous rather than the ad hoc measures. OpenEye Scientific Software (supported by Seascape in India) develops large-scale molecular modeling applications and toolkits in the areas of structure generation, docking, shape comparison, charge/electrostatics, chemical informatics and visualization.

The topics would include but are not limited to:

  • Understanding Protein, DNA, RNA and Carbohydrate structure
  • Description of the potential energy of a system of particles- Basics of Force fields
  • Principles and basic techniques in Molecular Dynamics simulation of biomolecules.
  • Small molecules as drug and their physico-chemical properties
  • Docking, lead identification and lead optimization


  • A.S.Kolaskar, University of Pune
  • Indira Ghosh, University of Pune
  • P. V. Balaji, I.I.T., Mumbai
  • Devapriya Choudhury, JNU, New Delhi
  • U.Sonawane, CDAC, Pune* to be confirmed
  • Matthew Stahl, OpenEye, USA
  • Gregory Warren, OpenEye, USA

Important dates
Last date for application:     December 3, 2007
Intimation of Selection:     December 5, 2007

Who should attend the workshop?
Scientists, teachers and research students working in academia & industry in various areas of life sciences who intend to apply Bioinformatics & Chemoinformatics approaches in their research or wish to contribute to the developments of drug designing. It is essential that the participants, who desire to attend this workshop, have a basic working knowledge of mathematics and Bioinformatics. Hands-on experience of using basic Bioinformatics tools and Unix OS with programming language would be advantageous.

Selection Criteria: Selection will be based on one-page write-up describing how this workshop will be beneficial to you in your work/research. Preferences will be given to the active researchers, teachers & Scientists.

Course Registration Fees
                Academic        Industry
Indian            INR 3000        INR 6000
SAARC            USD 350       
Other Countries        USD 550       
(Inclusive of course material and lunches during workshop)

Number of Participants: 40 (including 10 from Industry)

Participants will have to make their own arrangements of stay during the workshop. Guest house accommodation would be provided only in special cases.

Web site
For more details and registration please visit:


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Seascape ( is a computational science company offering software, R&D consulting and informatics services. Seascape R&D Network enables organizations engaged in nanosciences, materials, pharma, biotech and chemical research; to increase the cost-effectiveness and innovation potential of their R&D by tapping into scientific resources from India through contract, collaborative research projects.







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