Computer Simulation of Macromolecules
- 1 December 1990
- journal article
- research article
- Published by Taylor & Francis in Molecular Simulation
- Vol. 5 (5), 277-291
- https://doi.org/10.1080/08927029008022414
Abstract
Computer simulation techniques are now an essential part of modern structural molecular biology. They are used in many different ways in order to study the conformation, dynamics and interactions of proteins and nucleic acids. In this paper, I shall review several of these applications and then focus on three specific areas, namely the conformation and dynamics of proteins including the use of free energy perturbation methods to study mutant proteins, the conformation and dynamics of DNA and DNA-drug complexes, and the use of computers with parallel architectures. Although simulation of molecules as large and complex as proteins and nucleic acids may be considered a grand challenge in itself, there are even greater challenges for the future.Keywords
This publication has 15 references indexed in Scilit:
- Dynamical simulation of rate constants in protein-ligand interactionsProgress in Biophysics and Molecular Biology, 1988
- Crystallographic refinement by simulated annealingJournal of Molecular Biology, 1988
- The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambinJournal of the American Chemical Society, 1988
- Dynamics of Proteins and Nucleic AcidsPublished by Cambridge University Press (CUP) ,1987
- DNA structure and perturbation by drug bindingBiochemical Journal, 1987
- Structure refinement of oligonucleotides by molecular dynamics with nuclear overhauser effect interproton distance restraints: Application to 5′ d(C-G-T-A-C-G)2Journal of Molecular Biology, 1986
- Theoretical calculation of relative binding affinity in host-guest systems.Proceedings of the National Academy of Sciences, 1986
- Energy calculations on aspartic proteinases: human renin, endothiapepsin and its complex with an angiotensinogen fragment analogue, H-142Biochemical Society Transactions, 1985
- Solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coliJournal of Molecular Biology, 1985
- Comparison of simple potential functions for simulating liquid waterThe Journal of Chemical Physics, 1983