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Biochemistry, Biophysics, and Structural Biology Commons

Open Access. Powered by Scholars. Published by Universities.®

Molecular Biology

2009

Series

Adenylate kinase

Articles 1 - 1 of 1

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Iterative Cluster-Nma (Icnma): A Tool For Generating Conformational Transitions In Proteins, Adam D. Schuyler, Robert L. Jernigan, Pradman K. Qasba, Boopathy Ramakrishnan, Gregory S. Chirikjian Feb 2009

Iterative Cluster-Nma (Icnma): A Tool For Generating Conformational Transitions In Proteins, Adam D. Schuyler, Robert L. Jernigan, Pradman K. Qasba, Boopathy Ramakrishnan, Gregory S. Chirikjian

Biochemistry, Biophysics and Molecular Biology Publications

Computational models provide insight into the structure-function relationship in proteins. These approaches, especially those based on normal mode analysis, can identify the accessible motion space around a given equilibrium structure. The large magnitude, collective motions identified by these methods are often well aligned with the general direction of the expected conformational transitions. However, these motions cannot realistically be extrapolated beyond the local neighborhood of the starting conformation. In this paper, the icNMA method is presented for traversing the energy landscape from a starting conformation to a desired goal conformation. This is accomplished by allowing the evolving geometry of the intermediate ...