Tabu search based strategies for conformational search.

Julius-Maximillians-Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074 Würzburg, Germany.
The Journal of Physical Chemistry A (Impact Factor: 2.77). 09/2009; 113(43):11699-705. DOI: 10.1021/jp9028084
Source: PubMed

ABSTRACT This paper presents an application of the new nonlinear global optimization routine gradient only tabu search (GOTS) to conformational search problems. It is based on the tabu search strategy which tries to determine the global minimum of a function by the steepest descent-modest ascent strategy. The refinement of ranking procedure of the original GOTS method and the exploitation of simulated annealing elements are described, and the modifications of the GOTS algorithm necessary to adopt it to conformation searches are explained. The utility of the GOTS for conformational search problems is tested using various examples.

  • [Show abstract] [Hide abstract]
    ABSTRACT: The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. © 2014 Wiley Periodicals, Inc.
    Journal of Computational Chemistry 07/2014; · 3.60 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The proper description of explicit water shells is of enormous importance for all-atom calculations. We propose a new approach for the setup of water shells around proteins based on Tabu-Search global optimization and compare its efficiency with standard molecular dynamics protocols using the chignolin protein as a test case. Both algorithms generate reasonable water shells, but the new approach provides solvated systems with an increased water–enzyme interaction and offers further advantages. It enables a stepwise buildup of the solvent shell, so that the more important inner part can be prepared more carefully. It also allows the generation of solute structures which can be biased either toward the (experimental) starting structure or the underlying theoretical model, i.e., the employed force field.
    Journal of Chemical Theory and Computation 12/2012; 9(1):814–821. · 5.31 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: In this paper, a two-stage algorithm based on ordinal optimization (OO) theory is proposed to solve the booking limits problem with huge discrete solution space. First, a crude model with a small amount of simulation replications is used as a fitness evaluation in particle swarm optimization (PSO) algorithm to select N candidate solutions from solution space. Starting from the selected N candidate solutions, we then proceed with the optimal computing budget allocation (OCBA) technique to search for a good enough solution. The vector of good enough booking limits obtained by the proposed algorithm is promising in the aspects of solution quality and computational efficiency.
    Computer, Consumer and Control (IS3C), 2012 International Symposium on; 01/2012


1 Download