The DOI matches its Crossref record.
Validation of the general purpose tripos 5.2 force field
Abstract
A molecular mechanics force field implemented in the Sybyl program is described along with a statistical evaluation of its efficiency on a variety of compounds by analysis of internal coordinates and thermodynamic barriers. The goal of the force field is to provide good quality geometries and relative energies for a large variety of organic molecules by energy minimization. Performance in protein modeling was tested by minimizations starting from crystallographic coordinates for three cyclic hexapeptides in the crystal lattice with rms movements of 0.019 angstroms, 2.06 degrees, and 6.82 degrees for bond lengths, angles, and torsions, respectively, and an rms movement of 0.16 angstroms for heavy atoms. Isolated crambin was also analyzed with rms movements of 0.025 angstroms, 2.97 degrees, and 13.0 degrees for bond lengths, angles, and torsions respectively, and an rms movement of 0.42 angstroms for heavy atoms. Accuracy in calculating thermodynamic barriers was tested for 17 energy differences between conformers, 12 stereoisomers, and 15 torsional barriers. The rms errors were 0.8, 1.7, and 1.13 kcal/mol, respectively, for the three tests. Performance in general purpose applications was assessed by minimizing 76 diverse complex organic crystal structures, with and without randomization by coordinate truncation, with rms movements of 0.025 angstroms, 2.50 degrees, and 9.54 degrees for bond lengths, angles and torsions respectively, and an average rms movement of 0.192 angstroms for heavy atoms.
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Cited by
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network
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Activation and Inhibition of Adenylyl Cyclase Isoforms by Forskolin Analogs
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Theoretical Modeling of Zeolite Nanoparticle Surface Acidity for Heavy Oil Upgrading
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“Ligand interactions with residue 1029 were quantified in SYBYL 8.0 [30] via the Tripos Molecular Force Field [34] and Gasteiger-Marsili electrostatics [33].”
MethodInfluentialTakiguchi, K., Itoh, K., Shimmoto, M., Ozand, P. T., Doi, H., & Sakuraba, H. (2000) · Journal of Human Genetics · doi:10.1007/s100380070027 · Cited by 17
Scoring Functions for Protein–Ligand Interactions
Sotriffer, C. (2012) · Protein‐Ligand Interactions · doi:10.1002/9783527645947.ch12 · Cited by 16
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Metadata
- Authors
- Clark, M., Cramer, R. D., & Van Opdenbosch, N.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 1989-12
- Volume
- 10
- Issue
- 8
- Pages
- 982-1012
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2161239029
- Cited by
- 2,812
- References
- 0
- FWCI
- 5.21
- Type
- journal article
- Language
- en
- Open access
- closed
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