Guide to Biomolecular Simulations (Focus on Structural Biology)

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Applications of molecular dynamics in biophysics range over many areas. They are used in the structure determination of macromolecules with x-ray and NMR data, the modelling of unknown structures from their sequence, the study of enzyme mechanisms, the estimation of ligand-binding free energies, the evaluation of the role of conformational change in protein function, and drug design for targets of known structures.

The widespread application of molecular dynamics and related methodologies suggests that it would be useful to have available an introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of the field.

Biomolecular Simulations

This Guide to Biomolecular Simulations tries to fill this need. The Guide consists of six chapters which provide the fundamentals of the field and six chapters which introduce the reader to more specialized but important applications of the methodology. The book emerged from a biophysics course held at Harvard in the s and is therefore suited for standalone self-study as well as for classroom use …. And finally, a reader who successfully worked through the book obtained significant experience in using CHARMM, one of the most widely used molecular dynamics packages in biomolecular simulations.

JavaScript is currently disabled, this site works much better if you enable JavaScript in your browser. Chemistry Theoretical and Computational Chemistry. Focus on Structural Biology Free Preview. Computer simulations have become a standard tool for exploring biomolecules, often in conjunction with experimentally derived data Introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of biomolecular simulations The material on which the Hands-On Guide is based was developed and tested at Harvard University during the last 15 years Integrated exercises that involve the use of one of the premiere molecular dynamics programs CHARMM and the widely used graphics program CHARMM The fact that the programs used are widely distributed and generally available makes an introduction to them of importance for the future research career of students see more benefits.

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Biomolecular modelling and related Life Science disciplines – Bioexcel

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The art and science of cell biology ASCB 2. ASCB Newsletter 35 , 3—5 Berry, D. Molecular animation of cell death mediated by the fas pathway. STKE , tr1 Downey, A. Think Python O'Reilly Media, Lv, Z. Game on, science — how video game technology may help biologists tackle visualization challenges. Nature Methods in the press. Bhabha, G. Divergent evolution of protein conformational dynamics in dihydrofolate reductase.


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Ambient occlusion and edge cueing to enhance real time molecular visualization. Krebs, W.

The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Farrell, D. Comparison of pathways from the geometric targeting method and targeted molecular dynamics in nitrogen regulatory protein C. Tufte, E. Envisioning information. Vision Sci. Points of view: color coding. Nature Methods 7 , — Points of view: color blindness. Nature Methods 8 , — Points of view: avoiding color. McCloud, S. Protein dynamics. Miko, I. Nature Education [online] , Vale, R. The way things move: looking under the hood of molecular motor proteins. Science , 88—95 Carter, A. Crystal structure of the dynein motor domain. Saunders, Mura, C.

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An introduction to biomolecular graphics. PLoS Comput. Download references.

The authors thank E. Meng for editing, and G.