Tork: Conformational analysis method for molecules and complexes.
A conformational search method for organic molecules and bimolecular complexes is presented. The method, termed Tork, uses normal-mode analysis in bond-angle-torsion coordinates and focuses on a key subset of torsional coordinates to identify natural molecular motions that lead the initial conformation to new energy minima. New conformations are generated via distortion along these modes and their pairwise combinations, followed by energy minimization. For complexes, special treatment is accorded to the six coordinates that specify the position and orientation of one molecule relative to the other. Tests described here show that Tork is highly efficient for cyclic, acyclic, and mixed single molecules, as well as for host-guest complexes.
Chang
Chia-En
CE
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.
Gilson
Michael K
MK
D000465:Algorithms; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D003516:Cycloparaffins / Q000737:chemistry; D004988:Ethers, Cyclic / Q000737:chemistry; D008432:Mathematical Computing; D008610:Menthol / Q000737:chemistry; D008722:Methods; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D009795:Octanes / Q000737:chemistry; D009930:Organic Chemicals / Q000737:chemistry*; D010880:Piperidines / Q000737:chemistry; D013816:Thermodynamics
D003516:Cycloparaffins; D004988:Ethers, Cyclic; D009795:Octanes; D009930:Organic Chemicals; D010880:Piperidines; D008610:Menthol; C026728:octane