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Chapter 45: Computational Docking of Biomolecular Complexes with AutoDock—References

Freidman A.R., Roberts V.A., and Tainer J. A. 1994. Predicting molecular interactions and inducible complementarity: Fragment docking of Fab-peptide complexes. Proteins Struct. Func. Genet. 20: 15–24.

Goodsell D.S. and Olson A.J. 1990. Automated docking of substrates to proteins by simulated annealing. Proteins Struct. Funct. Genet. 8: 195–202.

Gschwend D.A., Good A.C., and Kuntz I.D. 1996. Molecular docking towards drug discovery. J. Mol. Recognit. 9: 175–186.

Halperin I., Ma B., Wolfson H., and Nussinov R. 2002. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins Struct. Funct. Genet. 47: 409–443.

Jackson R.C. 1995. Update on computer-aided drug design. Curr. Opin. Biotechnol. 6: 646–651.

Legge G.B., Morris G.M., Sanner M., Takada Y., Olson A.J., and Grynzpan F. 2002. Model of the αLβ2 integrin I-domain/ICAM-1 D1 interface suggests subtle changes in loop orientation determine ligand specificity. Proteins 48: 151–160.

Lengauer T. and Rarey M. 1996. Computational methods for biomolecular docking. Curr. Opin. Struct. Biol. 6: 402–406.

Lybrand T.P. 1995. Ligand-protein docking and rational drug design. Curr. Opin. Struct. Biol. 5: 224–228.

Marrone T.J., Briggs J.M., and McCammon J.A. 1997. Structure-based drug design: Computational advances. Annu. Rev. Pharmacol. Toxicol. 37: 71–90.

Morris G.M., Goodsell D.S., Huey R., and Olson A.J. 1996. Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. J. Comput. Aided Mol. Des. 10: 293–304.

Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., and Olson A.J. 1998. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19: 1639–1662.

Ollmann-Saphire E., Parren P., Pantophlet R., Zwick M.B., Morris G.M., Rudd P.M., Dwek R.A., Stanfield R.L., Burton D.R., and Wilson I.A. 2001. Crystal structure of a neutralizing human IgG against HIV-1: A template for vaccine design. Science 293: 1155–1159.

Osterberg F., Morris G.M., Sanner M.F., Olson A.J., and Goodsell D.S. 2002. Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins Struct. Funct. Genet. 46: 34–40.

Rosenfeld R., Vajda S., and Delisi C. 1995. Flexible docking and design. Annu. Rev. Biophys. Biomol. Struct. 24: 677–700.

Smith G.R. and Sternberg M.J.E. 2002. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12: 28–35.

Stoddard B.L. and Koshland D.E., Jr. 1992. Prediction of the structure of a receptor-protein complex using a binary docking method. Nature 358: 774–776.

Wlodawer A. and Erickson J.W. 1993. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62: 543–585.

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