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References (35)
-
N. Allinger, J. Tai (1965)
Organic Quantum Chemistry. IX. The Ultraviolet Spectra of Unsaturated Hydrocarbons. Woodward's Rules1,2Journal of the American Chemical Society, 87
-
P. Bash, N. Pattabiraman, Conrad Huang, T. Ferrin, R. Langridge (1983)
Van der Waals Surfaces in Molecular Modeling: Implementation with Real-Time Computer GraphicsScience, 222
-
F. Bernstein, T. Koetzle, G. Williams, E. Meyer, M. Brice, J. Rodgers, T. Singh, T. Shimanouchi, M. Tasumi (1977)
The Protein Data Bank: a computer-based archival file for macromolecular structures.Journal of molecular biology, 112 3
-
Alfredo Nola, H. Berendsen, O. Edholm (1984)
Free energy determination of polypeptide conformations generated by molecular dynamicsMacromolecules, 17
-
G. Chang, W. Guida, W. Still (1989)
An internal-coordinate Monte Carlo method for searching conformational spaceJournal of the American Chemical Society, 111
-
S. Weiner, P. Kollman, D. Nguyen, D. Case (1986)
An all atom force field for simulations of proteins and nucleic acidsJournal of Computational Chemistry, 7
-
W. Jorgensen, J. Tirado-Rives (1988)
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.Journal of the American Chemical Society, 110 6
-
AMPAC program number 506 -
N. Pattabiraman, M. Levitt, T. Ferrin, R. Langridge (1985)
Computer graphics in real‐time docking with energy calculation and minimizationJournal of Computational Chemistry, 6
-
N. Allinger (1977)
Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional termsJournal of the American Chemical Society, 99
-
Cambridge Scientific Computing, Inc -
(1984)
Berendsen and 0. Edholm, ibicl -
(1969)
Revue Francaise Informat -
M. Karplus (1959)
Contact Electron‐Spin Coupling of Nuclear Magnetic MomentsJournal of Chemical Physics, 30
-
L. Dresel (1966)
Elementary Numerical AnalysisThe Computer Journal, 9
-
M. Thomas, D. Emerson (1973)
The use of constraints in the evaluation of molecular strain energies specified by empirical valence-force potentialsJournal of Molecular Structure, 16
-
CPK firmware Version #A2.V03 -
M. Connolly (1983)
Solvent-accessible surfaces of proteins and nucleic acids.Science, 221 4612
-
C. Jaime, E. Ōsawa (1983)
A reparameterization of empirical hydrocarbon force field MM2 for improved performance in torsional energy surface calculationsTetrahedron, 39
-
(1977)
The most recent parameter set for MM2 was kindly provided by Professor N.L. Allinger at the University of Georgia -
E. Corey, W. Wipke, R. Cramer, W. Howe (1972)
Techniques for perception by a computer of synthetically significant structural features in complex moleculesJournal of the American Chemical Society, 94
-
M. Marsili, P. Floersheim, A. Dreiding (1983)
Generation and comparison of space-filling molecular modelsComput. Chem., 7
-
M. Lipton, W. Still (1988)
The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational spaceJournal of Computational Chemistry, 9
-
J. Nelder, R. Mead (1965)
A Simplex Method for Function MinimizationComput. J., 7
-
S. Weiner, P. Kollman, D. Case, U. Singh, C. Ghio, G. Alagona, S. Profeta, P. Weiner (1984)
A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINSJournal of the American Chemical Society, 106
-
B. Lee, F. Richards (1971)
The interpretation of protein structures: estimation of static accessibility.Journal of molecular biology, 55 3
-
J. Ponder, F. Richards (1987)
An efficient newton‐like method for molecular mechanics energy minimization of large moleculesJournal of Computational Chemistry, 8
-
C. Haasnoot, F. Leeuw, C. Altona (1980)
The relationship between proton-proton NMR coupling constants and substituent electronegativities—I : An empirical generalization of the karplus equation -
For an early use of bitwise set manipulations see -
MacroModel was developed with support and assistance from researchers at the following companies: Rohm & Haas -
(1984)
Linear and Nonlinear Programming, 2nd ed. -
W. Streett, D. Tildesley, G. Saville (1978)
Multiple time-step methods in molecular dynamicsMolecular Physics, 35
-
M. Karplus, J. Kushick (1981)
Method for estimating the configurational entropy of macromoleculesMacromolecules, 14
-
A. Bondi (1964)
van der Waals Volumes and RadiiThe Journal of Physical Chemistry, 68
-
D. Faber, C. Altona (1977)
UTAHB, a versatile programme package for the calculation of molecular properties by force field methodsComput. Chem., 1
- Publisher
- Wiley
- Copyright
- Copyright © 1990 John Wiley & Sons, Inc.
- ISSN
- 0192-8651
- eISSN
- 1096-987X
- DOI
- 10.1002/jcc.540110405
- Publisher site
- See Article on Publisher Site
Abstract
An integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described. The graphically controlled, atom‐based system allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state‐of‐the‐art molecular mechanics on any subset of up to 1,000 atoms. The system semiautomates the graphical construction and analysis of complex structures ranging from polycyclic organic molecules to biopolymers to mixed molecular complexes. We have placed emphasis on providing effective searches of conformational space by a number of different methods and on highly optimized molecular mechanics energy calculations using widely used force fields which are supplied as external files. Little experience is required to operate the system effectively and even novices can use it to carry out sophisticated modeling operations. The software has been designed to run on Digital Equipment Corporation VAX computers interfaced to a variety of graphics devices ranging from inexpensive monochrome terminals to the sophisticated graphics displays of the Evans & Sutherland PS300 series.
Journal
Journal of Computational Chemistry – Wiley
Published: May 1, 1990