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fpocket: online tools for protein ensemble pocket detection and tracking

2010; Oxford University Press; Volume: 38; Issue: Web Server Linguagem: Inglês

10.1093/nar/gkq383

1362-4962

Peter Schmidtke, Vincent Le Guilloux, Julien Maupetit, Pierre Tufféry,

Enzyme Structure and Function

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.