Key papers on DOT

Roberts, V. A. and Thompson, E. E. and Pique, M. E. and Perez, M. S. and Ten Eyck, L. F., (2013) “DOT2: Macromolecular docking with improved biophysical modelsJournal of Computational Chemistry, 34(20), 1743-1758, 30 July 2013
DOI: 10.1002/jcc.23304

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

Roberts, V. A., (2015) “C-terminal Domain of Integrase Binds Between the Two Active Sites J. Chem. Theory Comput., 11, 4500-4511.

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., 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.

M. Hammel, M. Rey, Y. Yu, R. S. Mani, S. Classen, M. Liu, M. E. Pique, S. Fang, B. L. Mahaney, M. Weinfeld, D. C. Schriemer, S. P. Lees-Miller, and J. A. Tainer, (2011) “XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair” J. Biol. Chem., 286, 32638-32650.

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, Victoria A. and Pique, Michael E. and Hsu, Simon and Li, Sheng, (2017) “Combining H/D Exchange Mass Spectrometry and Computational Docking To Derive the Structure of Protein-Protein ComplexesBiochemistry, 56, 6329-6342.

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.

Crevasse and protein shape analysis papers

Elaine E. Thompson, Alexandr P. Kornev, Natarajan Kannan, Choel Kim, Lynn F. Ten Eyck, and Susan S. Taylor (2009) “Comparative Surface Geometry of the Protein Kinase FamilyProtein Science, 18(10): 2016-2026.

J. C. Mitchell, R. Kerr, and L. F. Ten Eyck (2001) “Rapid Atomic Density Measures for Molecular Shape CharacterizationJ. Mol. Graph. Model., 19(3): 324-329.

Key paper on DEX

Matthew Hotchko, Ganesh S. Anand, Elizabeth A. Komives and Lynn F. Ten Eyck, (2005) “Automated Extraction of Backbone Deuteration Levels From Amide H/2H Mass Spectrometry Experiments” Protein Science, 15, 538-601. DOI: 10.1110/ps.051774906

Applications of DEXterity

Naughton K. L., Phan L., Leung E. M., Kautz R., Lin Q., Van Dyke Y., Marmiroli B., Sartori B., Arvai A., Li S., Pique M. E., Naeim M., Kerr J. P., Aquino M. J., Roberts V. A., Getzoff E. D., Zhu C., Bernstorff S., Gorodetsky A. A., (2016) “Self-Assembly of the Cephalopod Protein Reflectin” Adv. Mater., 28, 8405-8412.