Generating conformer ensembles using a multiobjective genetic algorithm.
The task of generating a nonredundant set of low-energy conformations for small molecules is of fundamental importance for many molecular modeling and drug-design methodologies. Several approaches to conformer generation have been published. Exhaustive searches suffer from the exponential growth of the search space with increasing degrees of conformational freedom (number of rotatable bonds). Stochastic algorithms do not suffer as much from the exponential increase of search space and provide a good coverage of the energy minima. Here, the use of a multiobjective genetic algorithm in the generation of conformer ensembles is investigated. Distance geometry is used to generate an initial conformer, which is then subject to geometric modifications encoded by the individuals of the genetic algorithm. The geometric modifications apply to torsion angles about rotatable bonds, stereochemistry of double bonds and tetrahedral chiral centers, and ring conformations. The geometric diversity of the evolving conformer ensemble is preserved by a fitness-sharing mechanism based on the root-mean-square distance of the atomic coordinates. Molecular symmetry is taken into account in the distance calculation. The geometric modifications introduce strain into the structures. The strain is relaxed using an MMFF94-like force field in a postprocessing step that also removes conformational duplicates and structures whose strain energy remains above a predefined window from the minimum energy value found in the set. The implementation, called Balloon, is available free of charge on the Internet ( http://www.abo.fi/~mivainio/balloon/).
Vainio
Mikko J
MJ
Structural Bioinformatics Laboratory, Department of Biochemistry and Pharmacy, Abo Akademi University, Tykistökatu 6A (BioCity), Turku, Finland. vikko.vainio@abo.fi
Johnson
Mark S
MS
D000465:Algorithms; D019295:Computational Biology; D018360:Crystallography, X-Ray; D016678:Genome / Q000235:genetics; D008957:Models, Genetic; D009690:Nucleic Acid Conformation