Journal article
Protein structure prediction force fields: parametrization with quasi-newtonian dynamics.
- Ulrich P Computational Chemistry (Physical Chemistry) ETH Zentrum, Zürich, Switzerland.
- Scott W
- van Gunsteren WF
- Torda AE
- 1997-03-01
Published in:
- Proteins. - 1997
English
We present an unusual method for parametrizing low-resolution force fields of the type used for protein structure prediction. Force field parameters were determined by assigning each a fictitious mass and using a quasi-molecular dynamics algorithm in parameter space. The quasi-energy term favored folded native structures and specifically penalized folded nonnative structures. The force field was generated after optimizing less than 70 adjustable parameters, but shows a strong ability to discriminate between native structures and compact misfolded alternatives. The functional form of the force field was chosen as in molecular mechanics and is not table-driven. It is continuous with continuous derivatives and is thus suitable for use with algorithms such as energy minimization or newtonian dynamics.
- Language
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- English
- Open access status
- closed
- Identifiers
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- DOI 10.1002/(sici)1097-0134(199703)27:3<367::aid-prot5>3.0.co;2-a
- PMID 9094739
- Persistent URL
- https://sonar.ch/global/documents/233569
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