DOCKING

Relevant publications

• Roberts, V. A., Pique, M. E., Ten Eyck, L. F., Li, S., (2013) "Predicting protein-DNA interactions by full search computational docking", Proteins, 81, 2106-2118.
• Roberts, V. A., Thompson, E. E., Pique, M. E., Perez, M. S., Ten Eyck, L. F., (2013) "DOT2: Macromolecular Docking With Improved Biophysical Models", J. Comput. Chem., 34, 1743-1758.
• Roberts, V. A., Pique, M. E., Hsu, S., Li, S., Slupphaug, G., Rambo, R. P., Jamison, J. W., Liu, T., Lee, J. H., Tainer, J. A., Ten Eyck, L. F., Woods, V. L. Jr., (2012) "Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase", Nuc. Acids. Res., 40, 6070-6081.
• Trinh, M.-H., Odorico, M., Pique, M. E., Teulon, J.-M., Roberts, V. A., Ten Eyck, L. F., Getzoff, E. D., Parot, P., Chen, S.-w. W., Pellequer, J.-L., (2012) "Computational reconstruction of multidomain proteins using atomic force microscopy data", Structure, 20, 113-120.
• Fan L., Fuss J.O., Cheng Q.J., Arvai A.S., Hammel M., Roberts V.A., Cooper P.K., Tainer J.A., (2008) "XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations", Cell, 133, 789-800.
• Fan, L. and Roberts, V. A., (2006) "Complex of Linker Histone H5 with the Nucleosome and Its Implications for Chromatin Packing", Proc. Natl. Acad. Sci. USA, 103, 8384-8389.
• Roberts, V. A., Case, D. A., and Tsui, V., (2004) "Predicting Interactions of Winged-Helix Transcription Factors with DNA", Proteins, 57, 172-187.
• 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., 47, 821-828.
• 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.