@article {2016|1661,
	title = {Hybridizing Rapidly Exploring Random Trees and Basin Hopping Yields an Improved Exploration of Energy Landscapes},
	journal = {J. Comput. Chem.},
	volume = {37},
	year = {2016},
	month = {mar},
	pages = {752},
	chapter = {739},
	abstract = {<p>The number of local minima of the potential energy landscape (PEL) of molecular systems generally grows exponentially with the number of degrees of freedom, so that a crucial property of PEL exploration algorithms is their ability to identify local minima, which are low lying and diverse. In this work, we pres- ent a new exploration algorithm, retaining the ability of basin hopping (BH) to identify local minima, and that of transition based rapidly exploring random trees (T-RRT) to foster the exploration of yet unexplored regions. This ability is obtained by interleaving calls to the extension procedures of BH and T- RRT, and we show tuning the balance between these two types of calls allows the algorithm to focus on low lying regions. Computational efficiency is obtained using state-of- the art data structures, in particular for searching approximate nearest neighbors in metric spaces. We present results for the BLN69, a protein model whose conformational space has dimension 207 and whose PEL has been studied exhaustively. On this system, we show that the propensity of our algorithm to explore low lying regions of the landscape significantly out- performs those of BH and T-RRT.</p>},
	doi = {10.1002/jcc.24256},
	author = {Christine A. Roth and Tom Dreyfus and Charles H. Robert and Fr{\'e}d{\'e}ric Cazals}
}
@article {2015|1679,
	title = {Conformational ensembles and sampled landscapes: analysis and comparison},
	journal = {J. Comp. Chem.},
	volume = {36},
	year = {2015},
	pages = {1213{\textendash}31},
	author = {Fr{\'e}d{\'e}ric Cazals and A Roth and T Dreyfus and D Mazauric and Charles H. Robert}
}
@article {2014|1772,
	title = {INRIA Tech Report: Conformational ensembles and sampled landscapes: analysis and comparison.},
	year = {2014},
	author = {Fr{\'e}d{\'e}ric Cazals and T. Dreyfus and D. Mazauric and A. Roth and Charles H. Robert}
}
@inbook {2013|1499,
	title = {Modeling macromolecular complexes: a journey across scales},
	booktitle = {Modeling in Computational Biology and Biomedicine: A Multidisciplinary Endeavor},
	year = {2013},
	note = {(in press)},
	publisher = {Springer-Verlag Berlin Heidelberg},
	organization = {Springer-Verlag Berlin Heidelberg},
	author = {Fr{\'e}d{\'e}ric Cazals and Tom Dreyfus and Charles H. Robert}
}
@article {2011|1653,
	title = {On the characterization and selection of diverse conformational ensembles with applications to flexible docking},
	journal = {Ieee/acm Trans. Comput. Biol. Bioinform.},
	volume = {8},
	year = {2011},
	pages = {487{\textendash}98},
	abstract = {<p>To address challenging flexible docking problems, a number of docking algorithms pregenerate large collections of candidate conformers. To remove the redundancy from such ensembles, a central problem in this context is to report a selection of conformers maximizing some geometric diversity criterion. We make three contributions to this problem. First, we resort to geometric optimization so as to report selections maximizing the molecular volume or molecular surface area (MSA) of the selection. Greedy strategies are developed, together with approximation bounds. Second, to assess the efficacy of our algorithms, we investigate two conformer ensembles corresponding to a flexible loop of four protein complexes. By focusing on the MSA of the selection, we show that our strategy matches the MSA of standard selection methods, but resorting to a number of conformers between one and two orders of magnitude smaller. This observation is qualitatively explained using the Betti numbers of the union of balls of the selection. Finally, we replace the conformer selection problem in the context of multiple-copy flexible docking. On the aforementioned systems, we show that using the loops selected by our strategy can improve the result of the docking process.</p>},
	doi = {10.1109/TCBB.2009.59},
	author = {Loriot, S{\'e}bastien and Sachdeva, Sushant and Bastard, Karine and Chantal Pr{\'e}vost and Fr{\'e}d{\'e}ric Cazals}
}
