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Tork - Conformational search method

 

Tork [1] is a powerful and flexible conformational search application which processes drug-like compounds and chemical host-guest complexes with arbitrary initial conformations. The method can efficiently generate low energy conformations of the compounds. Tork can be considered as a molecular level eigenvector-following technique [2,3]. However, it has several new features to accelerate the search, and is highly efficient for cyclic, acyclic, and mixed single molecules, as well as for host-guest complexes. Tork computes normal modes in key torsional coordinates, distorts the molecule along these modes singly and in various combinations, and then energy-minimizes the distorted conformations to yield new low-energy conformations. Normal modes are useful because they represent concerted "natural" motions that tend to lead to new low-energy structures.  The use of torsional, rather than Cartesian, coordinates markedly speeds the search because torsional coordinates generate more extensive bond rotations. Moreover, Tork has been implemented into Vconf, a conformational search software for drug-like compounds launched by Verachem, LLC

 

What is normal mode?

 

 

One of the low modes of flurbiprolen-cyclodextrin complex. See the ligand and several torsion angles move in concert.

image created by Dr. Wei Chen using VMD

 

1. Chang, C.-E and Gilson, M. K., Tork: A Conformational Analysis Method for Molecules and Complexes, J. of Comput Chem, 2003, 24, 1987-1998.

2. Kolossvary, I and W.C. Guida, Low mode search—an efficient, automated computational method for conformational analysis: application to cyclic and acyclic alkanes and cyclic peptides.  J. Am. Chem. Soc. 1996, 118, 5011-5019.

3. Cerjan, C. J. and W. H. Miller, On Finding Transition States, J. Chem. Phys. 1981, 75, 2800.

 

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