Molecular Modeling of Nucleic Acid Structure: Energy and Sampling
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Abstract
An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit discusses methods used to treat energy and to sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields. Curr. Protoc. Nucleic Acid Chem . 54:7.8.1?7.8.21. © 2013 by John Wiley & Sons, Inc.
Keywords: nucleic acid chemistry; nucleic acid structure and folding; structural analysis of biomolecules; experimental determination of structure; molecular modeling; molecular dynamics; force fields
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- The Energy Representation
- Beyond Energy Evaluation
- Summary
- Literature Cited
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Figure 7.8.1 Schematic of the interactions in a pairwise additive molecular mechanics force field. View Image -
Figure 7.8.2 Schematic representations of the sampling of various methods. These plots represent the energy of the system along an arbitrary reaction coordinate. The wells represent energy minima in the phase space. The state of the system is depicted by the location of the ball. (A ) Minimization. The system moves to the bottom of the nearest well and barriers are not overcome. (B ) Monte Carlo. Each configuration of the system is represented by a number and barrier crossing relates to the move set and total number of moves. (C ) Molecular dynamics. The state of the system evolves due to force according to Newton's equations of motion. In short simulations, large barriers will not be surmounted. View Image
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| Internet Resources | |
| http://www.ccl.net | |
| Lists of available software. | |
| http://www.netsci.org/Resources/Software/Modeling | |
| GAMESS Web site. | |
| http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid‐state_physics_software | |
| GAMESS‐UK Web site. | |
| http://www.msg.ameslab.gov/GAMESS/GAMESS.html | |
| Gaussian program Web site. | |
| http://www.cfs.dl.ac.uk/ | |
| Jaguar Web site. | |
| http://www.gaussian.com | |
| MolPro Web site. | |
| http://www.schrodinger.com | |
| NWChem. | |
| http://www.molpro.net | |
| Q‐chem Web site. | |
| http://www.nwchem‐sw.org/index.php/Main_Page | |
| Spartan Web site. | |
| http://www.q‐chem.com | |
| Terachem/Petachem. | |
| http://www.wavefun.com | |
| Turbomole. | |
| http://www.petachem.com/products.html | |
| ZINDO Web site. | |
| http://www.turbomole.com/ | |
| http://www.msi.com |
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