@article {2013|1976,
	title = {Reassessing buried surface areas in protein-protein complexes.},
	journal = {Protein Sci.},
	volume = {22},
	year = {2013},
	month = {aug},
	pages = {1453{\textendash}57},
	abstract = {<p>The buried surface area (BSA), which measures the size of the interface in a protein-protein complex may differ from the accessible surface area (ASA) lost upon association (which we call DSA), if conformation changes take place. To evaluate the DSA, we measure the ASA of the interface atoms in the bound and unbound states of the components of 144 protein-protein complexes taken from the Protein-Protein Interaction Affinity Database of Kastritis et al. (2011). We observe differences exceeding 20\%, and a systematic bias in the distribution. On average, the ASA calculated in the bound state of the components is 3.3\% greater than in their unbound state, and the BSA, 7\% greater than the DSA. The bias is observed even in complexes where the conformation changes are small. An examination of the bound and unbound structures points to a possible origin: local movements optimize contacts with the other component at the cost of internal contacts, and presumably also the binding free energy.</p>},
	keywords = {binding free energy, conformation changes, protein-protein interaction, solvent accessible surface},
	doi = {10.1002/pro.2330},
	author = {Chakravarty, Devlina and Guharoy, Mainak and Robert, Charles H. and Chakrabarti, Pinak and Janin, Jo{\"e}l}
}
@inbook {2011|1417,
	title = {Receptor Flexibility in Ligand Docking and Virtual Screening.},
	booktitle = {In-silico lead discovery},
	year = {2011},
	publisher = {Bentham Science Publishers},
	organization = {Bentham Science Publishers},
	author = {Maria A. Miteva and Charles H. Robert and J. D. Marechal and David Perahia}
}
@article {2009|1779,
	title = {Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers.},
	journal = {Biochemistry},
	volume = {48},
	number = {2},
	year = {2009},
	month = {jan},
	pages = {276{\textendash}288},
	publisher = {Department of Biological Sciences and Cell Differentiation and Development Center, Marshall University, Huntington, West Virginia 25755, USA.},
	abstract = {<p>Recent studies of the mechanisms involved in the regulation of gene expression in eukaryotic organisms depict a highly complex process requiring a coordinated rearrangement of numerous molecules to mediate DNA accessibility. Silencing in Saccharomyces cerevisiae involves the Sir family of proteins. Sir3p, originally described as repressing key areas of the yeast genome through interactions with the tails of histones H3 and H4, appears to have additional roles in that process, including involvement with a DNA binding component. Our in vitro studies focused on the characterization of Sir3p-nucleic acid interactions and their biological functions in Sir3p-mediated silencing using binding assays, EM imaging, and theoretical modeling. Our results suggest that the initial Sir3p recruitment is partially DNA-driven, highly cooperative, and dependent on nucleosomal features other than histone tails. The initial step appears to be rapidly followed by the spreading of silencing using linker DNA as a track.</p>},
	doi = {10.1021/bi801705g},
	author = {Nicholas L Adkins and Steve J McBryant and Cotteka N Johnson and Jennifer M Leidy and Christopher L Woodcock and Charles H Robert and Jeffrey C Hansen and Philippe T Georgel}
}
