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Protein structure prediction by global energy optimization

  • Chapter
Computer Simulation of Biomolecular Systems

Part of the book series: Computer Simulations of Biomolecular Systems ((CSBS,volume 3))

Abstract

The theoretical prediction of biomolecular structure from first principles and without the crutches of experimental restraints remains a dream. Most theoreticians agree that the answer is the global minimum of the free energy function [1,2], but disagree about strategies to find the minimum. Several schools of thought have formed over the years: dynamicists [3–11], minimalists [12–32], and synthesists [2,33–44]. Dynamicists believe that:sufficiently long simulations of a quasi-continuous trajectory of molecular dynamics of atomic models in vacuo or in water will solve the problem using new generations of computers, code parallelization [45,46], and optimized simulation techniques. Minimalists, unwilling to play power games and too impatient to wait until new generations of processors cover the next mile of a hundred-mile road, simplify the system by using a reduced atomic representation or a lattice, inventing a potential and then enjoying the luxury of always finding the global minimum of their energies as well as most of the other possible states for a chain of up to a hundred simplified residues [27,47]. The third school shares the impatience of minimalists, yet resists the temptation to use simple models since it appears that accuracy is a pivotal issue. Synthesists focus on the development of algorithms to replace molecular dynamics as a generator of conformational changes [42,43,48,35] and the design of methods of energy calculation which combine accuracy and speed.

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Authors and Affiliations

  1. The Skirball Institute of Biomolecular Medicine, Biochemistry Department, NYU Medical Center, New York University, 540 First Avenue, New York, NY, 10016, USA

    Ruben A. Abagyan

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  1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Zentrum, CH-8092, Zürich, Switzerland

    Wilfred F. van Gunsteren

  2. Amdyn Systems Inc., 28 Tower Street, 02143, Somerville, Massachusetts, USA

    Paul K. Weiner

  3. Zeneca Pharmaceuticals, Alderley Park, Macclesfied, SK10 4TG, Cheshire, UK

    Anthony J. Wilkinson

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Abagyan, R.A. (1997). Protein structure prediction by global energy optimization. In: van Gunsteren, W.F., Weiner, P.K., Wilkinson, A.J. (eds) Computer Simulation of Biomolecular Systems. Computer Simulations of Biomolecular Systems, vol 3. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-1120-3_14

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