Multi-protein docking for viral capsids

CVC Seminar Wed Oct 5 1:15-2:30pm ACES 4.304

Speaker: Muhibur Rasheed

Title: Multi-protein docking for viral capsids

Abstract:
Many biological functions are carried out by macromolecules or complexes composed of multiple proteins and nucleic acids. For example, the ribosome in E. Coli has 56 proteins, and viral capsids can be formed by hundreds of proteins. In this talk, we introduce the multi-protein docking problem as a tool to understand the structure, assembly and function of large complexes. The problem is NP-Hard in its most general formulation and hence researchers have made assumptions about the assembly process or restricted the problem to complexes having specific symmetries. We discuss current multi-protein docking techniques in terms of their search space, sampling technique and scoring functions and note that current techniques have many scopes for improvement. But we specifically choose the problem of viral capsid assembly due to its significance in anti-viral drug design. We discuss the current knowledge on the symmetry of the capsid structure and show how this symmetry can be applied to formulate a restricted class of multi-protein docking problem. We also show that how solutions of this problem can be used to identify leads for anti-viral drugs and to aid steady state analysis of assembly.

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