@article {2011|1848,
	title = {Free energy profiles along consensus normal modes provide insight into {HIV}-1 protease flap opening},
	journal = {J. Chem. Theor. Comput.},
	volume = {7},
	year = {2011},
	pages = {2348{\textendash}52},
	author = {Paulo R. Batista and Gaurav Pandey and Paulo M. Bisch and Paulo G. Pascutti and David Perahia and Charles H. Robert}
}
@article {2010|1736,
	title = {Consensus {M}odes, a robust description of protein collective motions from multiple-minima normal mode analysis{\textendash}application to the {HIV}-1 protease.},
	journal = {Phys. Chem. Chem. Phys.},
	volume = {12},
	year = {2010},
	month = {mar},
	pages = {2850{\textendash}2859},
	abstract = {<p>Protein flexibility is essential for enzymatic function, ligand binding, and protein-protein or protein-nucleic acid interactions. Normal mode analysis has increasingly been shown to be well suited for studying such flexibility, as it can be used to identify favorable structural deformations that correspond to functional motions. However, normal modes are strictly relevant to a single structure, reflecting a particular minimum on a complex energy surface, and are thus susceptible to artifacts. We describe a new theoretical framework for determining \&quot;consensus\&quot; normal modes from a set of related structures, such as those issuing from a short molecular dynamics simulation. This approach is more robust than standard normal mode analysis, and provides higher collectivity and symmetry properties. In an application to HIV-1 protease, the low-frequency consensus modes describe biologically relevant motions including flap opening and closing that can be used in interpreting structural changes accompanying the binding of widely differing inhibitors.</p>},
	doi = {10.1039/b919148h},
	author = {Paulo R. Batista and Charles H. Robert and Jean-Didier Mar{\'e}chal and M{\'e}riam Ben Hamida{\textendash}Reba\"{\i} and Paulo Pascutti and Paulo M. Bisch and David P. Perahia}
}
@article {2010|1788,
	title = {How does heparin prevent the p{H} inactivation of cathepsin {B}? Allosteric mechanism elucidated by docking and molecular dynamics.},
	journal = {Bmc Genomics},
	volume = {11, S5},
	year = {2010},
	author = {Mauricio G.S. Costa and Paulo R. Batista and Cl{\`a}udio S Shida and Charles H. Robert and Paulo M. Bisch and Pedro G. Pascutti}
}
