ISSN:
0192-8651
Keywords:
Chemistry
;
Theoretical, Physical and Computational Chemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
,
Computer Science
Notes:
An algorithm is presented for the refinement of reduced-model structures of proteins. A simulated annealing minimization is carried out in which the trial moves consist of the replacement of three-residue segments from a presorted library. The segments in the library are screened independently by their net end-to-end rotations so as to reproduce a distribution of conformations in the library similar to those in the ensemble. A general form of a look-up table contact potential is used to evaluate the free energy. This algorithm has been implemented on a parallel connection machine, on which a large number of molecules can be simultaneously simulated. The calculation of the pairwise distance matrix is distributed across the nodes of the machine to achieve an increase in performance and a reduction in the memory required on each node to store the potential table. The results of the refinement are shown for the test case of myoglobin, and the parallel performance is compared to that of a serial version of the algorithm. © 1996 by John Wiley & Sons, Inc.
Additional Material:
2 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/jcc.3
