Name
Title | ||
|---|---|---|
Optimizing ligand conformations in flexible protein targets: a multi-objective strategy |
Abstract | ||
|---|---|---|
Finding the orientation of a ligand (small molecule) with the lowest binding energy to the macromolecule (receptor) is a complex optimization problem, commonly called ligand–protein docking. This problem has been usually approached by minimizing a single objective that corresponds to the final free energy of binding. In this work, we propose a new multi-objective strategy focused on minimizing: (1) the root mean square deviation (RMSD) between the co-crystallized and predicted ligand atomic coordinates, and (2) the ligand–receptor intermolecular energy. This multi-objective strategy provides the molecular biologists with a range of solutions computing different RMSD scores and intermolecular energies. A set of representative multi-objective algorithms, namely NSGA-II, SMPSO, GDE3 and MOEA/D, have been evaluated in the scope of an extensive set of docking problems, which are featured by including HIV-proteases with flexible ARG8 side chains and their inhibitors. As use cases for biological validation, we have included a set of instances based on new retroviral inhibitors to HIV-proteases. The proposed multi-objective approach shows that the predictions of ligand’s pose can be promising in cases in which studies in silico are necessary to test new candidate drugs (or analogue drugs) to a given therapeutic target.
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Year | DOI | Venue |
|---|---|---|
2020 | 10.1007/s00500-019-04575-2 | Soft Computing |
Keywords | DocType | Volume |
Molecular docking, Multi-objective optimization, Metaheuristics | Journal | 24 |
Issue | ISSN | Citations |
14 | 1433-7479 | 0 |
PageRank | References | Authors |
0.34 | 0 | 5 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Esteban López-Camacho | 1 | 29 | 5.13 |
| María Jesús García-Godoy | 2 | 0 | 0.34 |
| José García-Nieto | 3 | 348 | 25.75 |
| Antonio J. Nebro | 4 | 1118 | 54.62 |
| José F. Aldana-Montes | 5 | 72 | 12.82 |