A series of molecular dynamics and homology modeling computer labs for an undergraduate molecular modeling course

Biochemistry and Molecular Biology Education

Volumn 38, Issue 4, 2010, Pages 216-223

  Elmore, Donald E ^a   Guayasamin, Ryann C ^a   Kieffer, Madeleine E ^a  

^a WELLESLEY COLLEGE   (United States)

Author keywords

Computational biology; Computers in research and teaching; Homology modeling; Molecular dynamics

Indexed keywords

EID: 77956850334     PISSN: 14708175     EISSN: 15393429     Source Type: Journal    
DOI: 10.1002/bmb.20396     Document Type: Article

References (20)

1. E. Lindahl, B. Hess, D. van der Spoel (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis, J. Mol. Mod. 7, 306-317.
2. A. Fiser, A. Sali (2003) MODELLER: Generation and refinement of homology-based protein structure models, Methods Enzymol. 374, 463-493.
3. N. Guex, M. C. Peitsch (1997) SWISS-MODEL and the Swiss-PDB Viewer: An environment for comparative protein modeling, Electrophoresis 18, 2714-2723.
4. W. L. DeLano (2002) The PyMOL molecular graphics system, DeLano Scientific, Palo Alto, CA.
5. D. A. Case, T. A. Darden, T. E. Cheatham, III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, M. Crowley, C. Ross, W. Walker, K. M. Zhang, K. M. Merz, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvary, K. F. Wong, F. Paesani, J. Vanicek, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D. H. Mathews, M. G. Seetin, C. Sagui, V. Babin, P. A. Kollman (2008) AMBER 10, University of California, San Francisco.
6. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem. 4, 187-217.
7. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipnot, R. D. Skeel, L. Kale, K. Schulten (2005) Scalable molecular dynamics with NAMD, J. Comput. Chem. 26, 1781-1802.
8. K. Arnold, L. Bordoli, J. Kopp, T. Schwede (2006) The SWISSMODEL workspace: A web-based environment for protein structure homology modelling, Bioinformatics 22, 195-201.
9. E. V. Anslyn, D. A. Dougherty (2006) Modern Physical Organic Chemistry, University Science, Sausalito, CA.
10. C. J. Cramer (2004) Essentials of Computational Chemistry: Theories and Models, Wiley, Chichester, England.
11. G. H. Grant, W. G. Richards (1995) Computational Chemistry, Oxford University Press, Oxford, England.
12. M. S. Madhusudhan, M. A. Marti-Renom, N. Eswar, B. John, U. Pieper, R. Karchin, M.-Y. Shen, A. Sali in J. M. Walker, Ed. (2005) The Proteomics Protocols Handbook, Humana Press, Totowa, NJ.
13. T. Schlick (2002) Molecular Modeling and Simulation: An Interdisciplinary Guide, Springer, New York, NY.
14. J. A. Maurer, D. E. Elmore, D. Clayton, L. Xiong, H. A. Lester, D. A. Dougherty (2008) Confirming the revised C-terminal domain of the MscL crystal structure, Biophys. J. 94, 4662-4667.
15. D. P. Tieleman, M. S. Sansom, H. J. Berendsen (1999) Alamethicin helices in a bilayer and in solution: Molecular dynamics simulations, Biophys. J. 76, 40-49.
16. P. Strop, S. L. Mayo (2000) Contribution of surface salt bridges to protein stability, Biochemistry 39, 1251-1255.
17. L. Z. Xu, R. Sanchez, A. Sali, N. Heintz (1996) Ligand specificity of brain lipid-binding protein, J. Biol. Chem. 271, 24711-24719.
18. N. Mirkovic, M. A. Marti-Renom, B. L. Weber, A. Sali, A. N. Monteiro (2004) Structure-based assessment of missense mutations in human BRCA1: Implications for breast and ovarian cancer predisposition, Cancer. Res. 64, 3790-3797.
19. G. Wu, A. Fiser, B. Ter Kuile, A. Sali, M. Muller (1999) Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase, Proc. Natl. Acad. Sci. USA 96, 6285-6290.
20. M. Y. Shen, A. Sali (2006) Statistical potential for assessment and prediction of protein structures, Protein. Sci. 15, 2507-2524.