DOCKING

Relevant publications

• Roberts, V. A., Case, D. A., and Tsui, V., "Predicting Interactions of Winged-Helix Transcription Factors with DNA" J. Mol. Biol., submitted.
• Adesokan, A. A., Roberts, V. A., Lee, K. W., Lins, R. D., and Briggs, J. M., (2003) "Prediction of HIV-1 Integrase/Viral DNA Interactions in the Catalytic Domain by Fast Molecular Docking" J. Med. Chem., in press.
• Law, D. S., Ten Eyck, L. F., Katzenelson, O., Tsigelny, I., Roberts, V. A., Pique, M. E., and Mitchell, J. C., (2003) "Finding Needles in Haystacks: Reranking DOT Results by Using Shape Complementarity, Cluster Analysis and Biological Information", Proteins, 52, 33-40.
• Mandell, J. G., Roberts, V. A., Pique, M. E., Kotlovyi, V., Mitchell, J. C., Nelson, E., Tsigelny, I., and Ten Eyck, L. F., (2001) "Protein Docking Using Continuum Electrostatics and Geometric Fit" Prot. Eng., 14, 105-113.
• Pellequer, J.-L., Zhao, B., Kao, H.-I., Bell, C. W., Li, K., Li, Q. X., Karu, A. E., and Roberts, V. A., (2000) "Stabilization of Bound Polycyclic Aromatic Hydrocarbons by a pi-Cation Interaction ", J. Mol. Biol., 302, 691-699.
• Roberts, V. A. and Pique, M. E., (1999) "Definition of the Interaction Domain for Cytochrome c on Cytochrome c Oxidase: III. Prediction of the Docked Complex by a Complete, Systematic Search", J. Biol. Chem., 274, 38051--38060.
• Jung, Y.-S., Roberts, V. A., Stout, C. D., and Burgess, B. K., (1998) "Complex Formation between Azotobacter vinelandii Ferrodoxin I and Its Physiological Electron Donor NADPH-Ferredoxin Reductase", J. Biol. Chem., 274, 2978-2987.
• Ten Eyck, L. F., Mandell, J., Roberts, V. A., and Pique, M. E., (1995) "Surveying Molecular Interactions With DOT", in Proceedings of the 1995 ACM/IEEE Supercomputing Conference, San Diego, IEEE Computer Society Press, Los Alamitos, California. available at the URL http://www.supercomp.org/sc95/proceedings/636_LTEN/SC95.HTM.
• Friedman, A. R., Roberts, V. A., and Tainer, J. A., (1994) "Predicting Molecular Interactions and Inducible Complementarity: Fragment Docking of Fab-Peptide Complexes", Proteins, 20, 15-24.
• Roberts, V. A., Freeman, H. C., Olson, A. J., Tainer, J. A., and Getzoff, E. D., (1991), "Electrostatic Orientation of the Electron-Transfer Complex Between Plastocyanin and Cytochrome c", J. Biol. Chem., 266, 13431-13441.