ISSN:
0948-5023
Keywords:
Genetic algorithm
;
Protein structure analysis
;
3D topology
Source:
Springer Online Journal Archives 1860-2000
Topics:
Chemistry and Pharmacology
Notes:
Abstract and Introduction The genetic algorithm exploits the principles of natural evolution. Solution trials are evolved by mutation, recombination and selection until they achieve near optimal solutions [1]. Our own approach has now been developed [2] after a general overview on the application potential for protein structure analysis [3] to a tool to delineate the three-dimensional topology for the mainchain of small proteins [4], no matter whether they are largely helical, are mixed or β-strand rich [5]. Results on several protein examples for these different modelling tasks are presented and compared with the experimentally observed structures (RMSDs are around 4.5-5.5 Å). To start a modelling trial only the protein sequence and knowledge of its secondary structure is required. The fittest folds obtained after the evolution at the end of the simulations yield the three dimensional models of the fold. Current limitations are protein size (generally less than 100 aminoacids), number of secondary structure elements [7-8] and irregular topologies (e.g. ferridoxins). Further, preliminary results from current simulations are illustrated. We now want to apply simple experimental or other information, which is available long before the three-dimensional structure of the protein becomes known, to refine the modelling of the protein fold and tackle also more difficult modelling examples by our tool.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/s0089460020304
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