27 February 2012 to 23 March 2012
Nordita
Europe/Stockholm timezone

SDAFlex: Simulating flexible macromolecules with Brownian dynamics

12 Mar 2012, 11:30
1h
132:028 (Nordita)

132:028

Nordita

Speaker

Dr Michael Martinez (Heidelberg Institute for Theoretical Studies)

Description

Studies of macromolecular interactions in solution are important for understanding biological activities such as protein-protein interactions in the regulation of signaling pathways. Brownian dynamics simulations are well adapted to the computation of kinetic rates of association between two or more macromolecules (often proteins). Furthermore they have been successfully used to perform protein-protein docking and to study protein-surface interactions and crowded macromolecular environments. However, Brownian dynamics simulations are often limited by the representation of macromolecules as rigid bodies. We have addressed this limitation by extending the SDA6 (Simulation of Diffusional Association [Gabdouline, Wade, 1997]) software to incorporate flexibility of interacting macromolecules. The software incorporates features from the original SDA6 software as well as the SDAMM (SDAMM [Mereghetti, Gabdouline, Wade, 2010] ) software designed to study crowded macromolecular environments. The new software, SDAFlex, has been written using an object-oriented approach, uses less memory and can be run in parallel on shared-memory architecture hardware. SDAFlex simulates flexibility by switching between predefined macromolecular conformations determined by normal mode analysis, NMR or molecular dynamics. Two schemes for accepting conformational switches are implemented: the first which minimises the total system energy; the second a Monte-Carlo algorithm. SDAFlex enables fast generation of docking poses using multiple-conformations and calculation of kinetic rates of association when flexibility and/or a crowded environments are accounted for.

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