Boojala Vijay B. Reddy
(Queens College and Graduate Center, CUNY)

"Bioinformatics of Protein Sequences and
Structures to Understand their Folding,
Function and Interactions"

Proteins constitute most of the living cells dry mass. These are building blocks and execute all the network of functions of the living cells, have surfaces to promote chemical reactions, form channels, pumps and carry messages. These are tiny molecular machines with moving parts such as antibodies, toxins, hormones, antifreeze molecules and also sources of luminescence. Computational analyses of exponentially growing protein molecular data of several forms: as sequence of linear amino acids, as 3D structures and as microarray expression data has interesting hidden functional information. It is challenging for computational scientists to analyze these databases to extract useful information. I briefly introduce the proteins and their amazing characteristics. I will then present the computational methods we developed recently to identify conserved key amino acid positions which are shown to have implications in protein folding, function and protein-protein interaction site predictions. My presentation basically shows how we have used the evolutionary information of several related protein sequences and structures to predict the functional sites on the proteins which is useful in de novo molecular design and drug designing applications. I will also present a overview of some of my future research interests in computational study of biomolecules, and in developing improved methods for protein structure modeling.

References

• Reddy BVB, Kaznessis Y (2005) A Quantitative analysis of amino acid position conservation in interface regions of protein-protein hetrocomplexes. (submitted).
• Duan, Y. Reddy BVB, Kaznessis Y (2005) Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions.
  Protein Science 14: 316 - 328.
• Vicatos S, Reddy BVB, Kaznessis, Y. (2005)  Prediction of distant residue contacts with the use of evolutionary information from PFAM database.
  Proteins: Struct. Func. and Bioinfo 58: 935 - 949.
• Reddy BVB, Li WW, Bourne P. (2002) Use of Conserved Key Amino Acid Positions to Morph Protein Folds.
  Biopolymers. 64: 139 – 145.
• Li WW, Reddy BVB, Tate J, Shindyal I, Bourne P (2002)  CKAAPs: A Conserved Key Amino Acid Positions DataBase. 
  Nucleic Acids Research. 30: 409 - 411.
• Li WW, Reddy BVB, Shindyal I, Bourne P (2001)  CKAAPs: A Conserved Key Amino Acid Positions DataBase. 
  Nucleic Acids Research. 29: 329-31.
• Reddy BVB, Li WW, Shindyal I, Bourne P (2001) Conserved Key amino acid Positions (CKAAPs) derived from analysis of common substructures in proteins.
  Proteins: Struct. Func. and Genetics. 42: 148-63.

The Colloquium is supported by generous contributions from the Bloomberg, Information Builders, Inc. and Netlogic, Inc.