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Studies of molecular docking between fibroblast growth factor and heparin using generalized simulated annealing
Author(s) -
da Rocha Pita Samuel Silva,
Fernandes Tácio Vinício Amorim,
Caffarena Ernesto Raul,
Pascutti Pedro Geraldo
Publication year - 2008
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.21731
Subject(s) - simulated annealing , docking (animal) , ranging , computer science , chemistry , algorithm , statistical physics , physics , medicine , telecommunications , nursing
Abstract Since the middle 70s, the main molecular docking problem consists in limitations to treat adequately the degrees of freedom of protein (or a receptor) due to the energy landscape roughness and the high computational cost. Until recently, only few algorithms considering flexible simultaneously both ligand and receptor at low computational cost were developed. As a recent proposed Statistical Mechanics, generalized simulated annealing (GSA) has been employed at diverse works concerning global optimization problems. In this work, we used this method exploring the molecular docking problem taking into account the FGF‐2 and heparin complex. Since the requirements of an efficient docking algorithm are accuracy and velocity, we tested the influence of GSA parameters q A (new configuration acceptance index), q V (energy surface visiting index), and q T (temperature decreasing control) on the performance of GSADOCK program. Our simulations showed that as temperature parameter q T increases, q A parameter follows this behavior in the interval ranging from 1.1 to 2.3. We found that the GSA parameters have the best performance for the q A values ranging from 1.1 to 1.3, q V values from 1.3 to 1.5, and q T values from 1.1 to 1.7. Most of good q V values were equal or next the good q T values. Finally, the implemented algorithm is trustworthy and can be employed as a tool of molecular modeling methods. The final version of the program will be free of charge and will be accessible at our home‐page or could be requested to the authors for e‐mail. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008