By Hans-Dieter Höltje
Written by way of skilled specialists in molecular modeling, this books describes the fundamentals to the level that's useful if one desires to have the ability to reliably pass judgement on the implications from molecular modeling calculations.
Its major target is the outline of some of the pitfalls to be shunned. with out pointless overhead it leads the reader from easy calculations on small molecules to the modeling of proteins and different appropriate biomolecules.
A textbook for novices in addition to a useful reference for all these facing molecular modeling of their day-by-day paintings!
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Additional resources for Molecular Modeling: Basic Principles and Applications
J. Comput. Chem. 4,187-217 (1983). C. Molecular dynamics simulations: techniques and applications to proteins. In: Molecular Dynamics and Protein Structure. Hermans, J. ). Polycrystal Books Service: Western Springs, Illinois; 5-14 (1985). (131 Hopfinger, A. , and Pearlstein, R. A. J. Comput. Chem. 48-99 (1984). T. Proc. Nail Acad. 85,535G5354 (1988). [ 151 Bowen, J. , and Allinger, N. L. Molecular Mechanics: The Art and Science of Parameterization. 2. Lipkowitz, K. , and Boyd, D. B. ). VCH: New York; 81-97 (1991).
3 Conformational Analysis 35 In some cases, however, it is not sufficient to minimize the sampled conformations in order to reach the final minimum conformation. The intention of the high-temperature dynamics simulation is to provide the molecule with enough kinetic energy to cross energy barriers between different conformations. However, during the simulation the molecule can occupy extremely distorted geometries which sometimes cannot be relaxed by a simple minimization procedure. If this occurs it is recommended to perform a high-temperature annealed molecular dynamics simulation .
ACS Monograph 177. American Chemical Society: Washington D. C. 1982. T. New Approaches to Empirical Force Fields. In: Reviews in Computational Chemistry,Vol. 2. Lipkowitz, K. , and Boyd, D. B. ). VCH: New York; 99-164 (1991). , and Van Opdenbosch, N. J. Comput. Chem. 10,982-1012 (1989). T. Proteins: Structure, Function and Genetics 4,3147 (1988). [ I l l Brooks, B. , Bruccoleri, R. , Olafson, B. , States, D. , and Karplus, M. J. Comput. Chem. 4,187-217 (1983). C. Molecular dynamics simulations: techniques and applications to proteins.