Evaluation of GalaxyDock Based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies.
J Chem Inf Model
; 56(6): 988-95, 2016 06 27.
Article
en En
| MEDLINE
| ID: mdl-26583962
ABSTRACT
We analyze the results of the GalaxyDock protein-ligand docking program in the two recent experiments of Community Structure-Activity Resource (CSAR), CSAR 2013 and 2014. GalaxyDock performs global optimization of a modified AutoDock3 energy function by employing the conformational space annealing method. The energy function of GalaxyDock is quite sensitive to atomic clashes. Such energy functions can be effective for sampling physically correct conformations but may not be effective for scoring when conformations are not fully optimized. In phase 1 of CSAR 2013, we successfully selected all four true binders of digoxigenin along with three false positives. However, the energy values were rather high due to insufficient optimization of the conformations docked to homology models. A posteriori relaxation of the model complex structures by GalaxyRefine improved the docking energy values and differentiated the true binders from the false positives better. In the scoring test of CSAR 2013 phase 2, we selected the best poses for each of the two targets. The results of CSAR 2013 phase 3 suggested that an improved method for generating initial conformations for GalaxyDock is necessary for targets involving bulky ligands. Finally, combining existing binding information with GalaxyDock energy-based optimization may be needed for more accurate binding affinity prediction.
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Simulación del Acoplamiento Molecular
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
J Chem Inf Model
Asunto de la revista:
INFORMATICA MEDICA
/
QUIMICA
Año:
2016
Tipo del documento:
Article