Molecular Modeling of Proteins (Methods in Molecular Biology)

Molecular modeling has passed through a impressive transformation within the final twenty years. This booklet presents thorough introductions and a compilation of step by step tools acceptable to difficulties confronted through non-specialists – particularly these new to the software program applications utilized in molecular modeling. tips about troubleshooting and warding off universal pitfalls are integrated within the e-book, besides chapters masking a variety of matters. hyperlinks to downloadable software program also are provided.

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Biophys. J. eighty two, 676–683. 31. Arinaminpathy, Y. , Sansom, M. S. P. , and Biggin, P. C. (2006) Binding website flexibility: Molecular simulation of partial and whole agonists inside of a glutamate receptor. Mol. Pharm. sixty nine, 11–18. 32. Kaye, L. S. , Sansom, M. S. P. , and Biggin, P. C. (2006) Molecular dynamics simulations of an NMDA Receptor. J. Biol. Chem 281, 12736–12742. 33. Mouritsen, O. G. , and Jorgensen, okay. (1997) Small-scale lipid-membrane constitution: simulation as opposed to scan. Curr. Opin. Struct. Biol. 7, 518–527. 34. Feller, S. E. (2000) Molecular dynamics simulations of lipid bilayers. Curr. Opin. Coll. Interface Sci. five, 217–223. 35. Scott, H. L. (2002) Modeling the lipid section of membranes. Curr. Opin. Struct. Biol. 12, 495–502. 36. Tieleman, D. P. , Marrink, S. J. , and Berendsen, H. J. C. (1997) a working laptop or computer viewpoint of membranes: Molecular dynamics stories of lipid bilayer structures. Biochim. Biophys. Acta 1331, 235–270. 37. Belohorcova, okay. , Davis, J. H. , Woolf, T. B. , and Roux, B. (1997) constitution and dynamics of an amphiphilic peptide in a lipid bilayer: a molecular dynamics learn. Biophys. J. seventy three, 3039–3055. 38. Woolf, T. B. , and Roux, B. (1996) constitution, energetics, and dynamics of lipid-protein interactions - a molecular-dynamics learn of the gramicidin-A channel in a DMPC bilayer. Proteins: Struc. Func. Genet. 24, 92–114. 39. Faraldo-G´omez, J. D. , Smith, G. R. , and Sansom, M. S. P. (2002) constructing and optimization of membrane protein simulations. Eur. Biophys. J. 31, 217–227. forty. Lindahl, E. , Hess, B. , and van der Spoel, D. (2001) GROMACS three. zero: A package deal for molecular simulation and trajectory research. J. Mol. version 7, 306–317. forty-one. Humphrey, W. , Dalke, A. , and Schulten, ok. (1996) VMD—Visual molecular dynamics. J. Molec. Graph. 14, 33–38. forty two. Phillips, J. C. , Braun, R. , Wang, W. , Gumbart, J. , Tajkhorshid, E. , Villa, E. , Chipot, C. , Skeel, R. D. , Kale, L. , and Schulten, ok. (2005) Scalable molecular dynamics with NAMD. J. Comp. Chem. 26, 1781–17802. forty three. Christen, M. , and Van Gunsteren, W. F. (2006) Multigraining: An set of rules for simultaneous fine-grained and coarse-grained simulation of molecular structures. J. Chem. Phys. 124, 154106. 1-06. 7. forty four. Chang, R. , Ayton, G. S. , and Voth, G. A. (2005) Multiscale coupling of mesoscopic and atomistic-level lipid bilayer simulations. J. Chem. Phys. 122, 244716. forty five. Shi, Q. , Izvekov, S. , and Voth, G. A. (2006) combined atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel. J. Phys. Chem. B. one hundred ten, 15045– 15048. forty six. Smit, B. , Hilbers, A. J. , Esselink, okay. , Rupert, L. A. M. , Van Os, N. M. , and Schlijper, G. (1990) desktop simulations of a water/oil interface within the presence of micelles. Nature 348, 624–625. forty seven. Murtola, T. , Falck, E. , Patra, M. , Karttunen, M. , and Vattulainen, I. (2004) Coarse-grained version for phospholipid/cholesterol bilayer. J. Chem. Phys. 121, 9156–9165. a hundred and sixty P. C. Biggin, P. J. Bond forty eight. Stevens, M. J. , Hoh, J. H. , and Woolf, T. B. (2003) Insights into the molecular mechanism of membrane fusion from simulation: facts for the organization of splayed tails. Phys. Rev. Lett. ninety one, 188102. 1-02. four. forty nine. Shelley, J. C.

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