A genetic algorithm for the ligand-protein docking problem
Genet. mol. biol
;
27(4): 605-610, Dec. 2004. ilus, tab
Article
Dans Anglais
| LILACS
| ID: lil-391236
ABSTRACT
We analyzed the performance of a real coded "steady-state" genetic algorithm (SSGA) using a grid-based methodology in docking five HIV-1 protease-ligand complexes having known three-dimensional structures. All ligands tested are highly flexible, having more than 10 conformational degrees of freedom. The SSGA was tested for the rigid and flexible ligand docking cases. The implemented genetic algorithm was able to dock successfully rigid and flexible ligand molecules, but with a decreasing performance when the number of ligand conformational degrees of freedom increased. The docked lowest-energy structures have root mean square deviation (RMSD) with respect to the corresponding experimental crystallographic structure ranging from 0.037 Å to 0.090 Å in the rigid docking, and 0.420 Å to 1.943 Å in the flexible docking. We found that not only the number of ligand conformational degrees of freedom is an important aspect to the algorithm performance, but also that the more internal dihedral angles are critical. Furthermore, our results showed that the initial population distribution can be relevant for the algorithm performance.
Texte intégral:
Disponible
Indice:
LILAS (Amériques)
Sujet Principal:
Liaison aux protéines
/
Algorithmes
/
Protéines
Type d'étude:
Étude pronostique
langue:
Anglais
Texte intégral:
Genet. mol. biol
Thème du journal:
Génétique
Année:
2004
Type:
Article
/
descriptif de projet
Pays d'affiliation:
Brésil
Institution/Pays d'affiliation:
Laboratório Nacional de Computação Científica/BR
Documents relatifs à ce sujet
MEDLINE
...
LILACS
LIS