Flexibility and Mobility in Biomolecules

Molecular dynamics is unable to explore the conformations of large protein complexes, viral capsids etc. Using Lagrange constraints for covalent bonds, hydrogen bonds, hydrophobic tethers, the rigid regions and the flexible joints between them can be found using graph theory. This input is then used as the basis for a geometric based simulation using a Monte Carlo dynamics that uses ghost templates to efficiently guide rigid clusters through conformational space via the flexible joints between them. This approach also incorporates van der Waals overlaps to maintain good local stereochemistry. The generation of a new protein conformation typically requires about 100 milliseconds CPU time

Mike Thorpe, Arizona State University

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