fpocket: Online tools for protein ensemble pocket detection and tracking

Abstract

Computational small-molecule binding site detection has several important applications in the biomedical field. Notable interests are the identification of cavities for structure-based drug discovery or functional annotation of structures. fpocket is a small-molecule pocket detection program, relying on the geometric α-sphere theory. The fpocket web server allows: (i) candidate pocket detection-fpocket; (ii) pocket tracking during molecular dynamics, in order to provide insights into pocket dynamics-mdpocket; and (iii) a transposition of mdpocket to the combined analysis of homologous structures-hpocket. These complementary online tools allow to tackle various questions related to the identification and annotation of functional and allosteric sites, transient pockets and pocket preservation within evolution of structural families. The server and documentation are freely available at http://bioserv.rpbs.univ-paris-diderot.fr/fpocket. © The Author(s) 2010. Published by Oxford University Press.