Guliaev AB, Cheng S, Hang B. Protein dynamics via computational microscope. World J Methodol 2012; 2(6): 42-49 [PMID: 25237616 DOI: 10.5662/wjm.v2.i6.42]
Corresponding Author of This Article
Anton B Guliaev, Assistant Professor, Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, United States. guliaev@sfsu.edu
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Review
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World J Methodol. Dec 26, 2012; 2(6): 42-49 Published online Dec 26, 2012. doi: 10.5662/wjm.v2.i6.42
Protein dynamics via computational microscope
Anton B Guliaev, Senping Cheng, Bo Hang
Anton B Guliaev, Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, United States
Senping Cheng, Pan-Pacific Biopharma, Inc., San Francisco, CA 94105, United States
Bo Hang, Department of Cancer and DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
Author contributions: Guliaev AB is a primary and the corresponding author for the manuscript; Cheng S and Hang B are co-authors and contributed to the discussion and provided critical reading of the manuscript.
Correspondence to: Anton B Guliaev, Assistant Professor, Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, United States. guliaev@sfsu.edu
Telephone: +1-415-4052961 Fax: +1-415- 3382384
Received: September 29, 2012 Revised: November 19, 2012 Accepted: November 28, 2012 Published online: December 26, 2012
Abstract
The purpose of this overview is to provide a concise introduction to the methodology and current advances in molecular dynamics (MD) simulations. MD simulations emerged as a powerful and popular tool to study dynamic behavior of proteins and macromolecule complexes at the atomic resolution. This approach can extend static structural data, such as X-ray crystallography, into dynamic domains with realistic timescales (up to millisecond) and high precision, therefore becoming a veritable computational microscope. This perspective covers current advances and methodology in the simulation of protein folding and drug design as illustrated by several important published examples. Overall, recent progress in the simulation field points to the direction that MD will have significant impact on molecular biology and pharmaceutical science.
