fpocket: online tools for protein ensemble pocket detection and tracking.
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 alpha-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.
Schmidtke
Peter
P
Departament de Fisicoquimica and Institut de Biomedicina, Facultat de Farmacia, Universitat de Barcelona, 08028, Barcelona, Spain.
Le Guilloux
Vincent
V
Maupetit
Julien
J
Tufféry
Pierre
P
D001665:Binding Sites; D006454:Hemoglobins / Q000737:chemistry; D020407:Internet; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D012984:Software; D040681:Structural Homology, Protein; D014584:User-Computer Interface
D006454:Hemoglobins; D008024:Ligands