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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
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. 