@article {2012|1934,
	title = {{ATTRACT} and {PTOOLS}: {O}pen source programs for protein-protein docking},
	journal = {Methods Mol. Biol.},
	volume = {819},
	year = {2012},
	pages = {221{\textendash}232},
	abstract = {<p>The prediction of the structure of protein-protein complexes based on structures or structural models of isolated partners is of increasing importance for structural biology and bioinformatics. The ATTRACT program can be used to perform systematic docking searches based on docking energy minimization. It is part of the object-oriented PTools library written in Python and C++. The library contains various routines to manipulate protein structures, to prepare and perform docking searches as well as analyzing docking results. It also intended to facilitate further methodological developments in the area of macromolecular docking that can be easily integrated. Here, we describe the application of PTools to perform systematic docking searches and to analyze the results. In addition, the possibility to perform multi-component docking will also be presented.</p>
},
	doi = {10.1007/978-1-61779-465-0_15},
	author = {Schneider, S. and A Saladin and Fiorucci, S. and Chantal Pr{\'e}vost and Martin Zacharias}
}
@article {2011|1654,
	title = {Accounting for large amplitude protein deformation during in silico macromolecular docking},
	journal = {Int. J. Mol. Sci.},
	volume = {12},
	year = {2011},
	pages = {1316{\textendash}33},
	abstract = {<p>Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.</p>},
	keywords = {flexibility, macromolecular docking, protein loops and domains},
	doi = {10.3390/ijms12021316},
	author = {Bastard, Karine and A Saladin and Chantal Pr{\'e}vost}
}
