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Towards protein folding with evolutionary techniques
Author(s) -
Koskowski Florian,
Hartke Bernd
Publication year - 2005
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20254
Subject(s) - dihedral angle , force field (fiction) , protein secondary structure , folding (dsp implementation) , protein folding , sequence (biology) , computer science , algorithm , random coil , protein data bank , protein tertiary structure , protein structure , chemistry , artificial intelligence , engineering , structural engineering , molecule , hydrogen bond , biochemistry , organic chemistry
We present design details and first tests of a new evolutionary algorithm approach to ab initio protein folding. It does not focus on dihedral angles exclusively, but mainly operates on introduction, extension, break‐up, and destruction of secondary structure elements, given as correlated dihedral angle values. In first test applications to polyalanines (up to 60 residues) and random primary sequences (up to 40 residues), we demonstrate that this use of prior knowledge is well balanced: On the one hand, it ensures quick introduction of secondary structure elements if they are favorable for a given primary sequence, but still allows for efficient location of pure random coil solutions without enforcing any secondary structure elements, if folds of this type are preferred by the given primary sequence. Furthermore, the algorithm is clearly able to pack several secondary structure elements into favorable tertiary structure arrangements, although no part of the algorithm is explicitly designed to do this. In first test examples on real‐life peptides between 21 and 44 residues from the Protein Data Bank, the quality of the results depends on the force field used (as expected); nevertheless, we can show that the algorithm is able to find structures in good agreement with the targets easily and consistently, if the force field allows for that. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1169–1179, 2005