System for prediction of protein side-chain conformation and met

Details System for prediction of protein side-chain conformation and met System for prediction of protein side-chain conformation and met

1994-12-09

1998-03-03

Cosimano, Edward R.

Boots, shoes, and leggings

364578, G06F 17159, G01N 3300, G01N 3700

Patent

active

057242526

ABSTRACT:
In the prediction of side-chain conformation of protein, conformations are predicted by describing a candidate conformation in the form of an array whose components are the torsion angles of a side chain, subjecting a plurality of solution candidates to evaluation, increasing side chains in a stepwise manner, judging the appropriateness of a solution candidate based upon degree of its van der Waals contact, and generating a new solution candidate by changing torsion angle to an arbitrary value or by interchanging the components of the torsion-angle arrays of two solution candidates. Further, the foregoing processing is executed with respect to the main-chain conformation whenever a side-chain conformation corresponding to one amino acid residue is constructed, and construction of all side-chain conformations is performed in incremental fashion.

REFERENCES:
patent: 5526281 (1996-06-01), Chapman et al.
patent: 5553004 (1996-09-01), Gronbech-Jensen et al.
J. Mol. Biol., 1991, vol. 217, pp. 373-388, Christopher Lee, et al., "Prediction of Protein Side-Chain Conformation by Packing Optimization".
Proteins: Structure, Function, and Genetics, vol. 2, pp. 330-339, 1987, Hiroshi Iijima, et al., "Calibration of Effective Van Der Waals Atomic Contact Radii for Proteins and Peptides".
Journal of Computational Chemistry, vol. 5, No. 2, pp. 129-145, 1984, U. Chandra Singh, et al., "An Approach to Computing Electrostatic Charges for Molecules".
Journal of Computational Chemistry, vol. 10, No. 8, pp. 982-1012, Matthew Clark, et al., "Validation of the General Purpose Tripos 5.2 Force Field".
Proceedings of The first IEEE Conference on Evolutionary Computation, Jun. 1994, vol. 1, Hiroshi Iijima, et al., "Incremental Prediction of the Side-Chain Conformation of Proteins by a Genetic Algorithm", pp. 362-367.

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