CCMS Publications

Key papers on DOT

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.

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.

Application of DOT to protein-DNA interactions

Fan, L. and Roberts, V. A., (2006) "Complex of linker Histone H5 with the Nucleosome and Its Implications for Chromatin Packing", Proc. Nat. Acad. Sci. U.S.A., 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.

Application of DOT to protein-protein interactions

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.

Additional methods/evaluation papers

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.