Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes
Docking using different programs provides more reliable information about the interaction of molecules than data obtained in a single program. An exponential consensus ranking (ECR) was developed to combine scoring functions across docking programs differing in efficiencies and scales of measurement...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | MethodsX |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2215016122001686 |
| _version_ | 1811201269954510848 |
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| author | Fabiani Triches Francieli Triches Cilene Lino de Oliveira |
| author_facet | Fabiani Triches Francieli Triches Cilene Lino de Oliveira |
| author_sort | Fabiani Triches |
| collection | DOAJ |
| description | Docking using different programs provides more reliable information about the interaction of molecules than data obtained in a single program. An exponential consensus ranking (ECR) was developed to combine scoring functions across docking programs differing in efficiencies and scales of measurements. The ECR method was adapted to merge results of re- and cross-dockings (i.e., ensemble docking) made in multiple docking programs. Adapted ECR consisted of four consecutive steps: 1- determination of scoring functions for a ligand with a series of macromolecules in multiple docking programs; 2- ranking of the scoring functions per macromolecule in each program; 3- combining the ranking across the programs creating a ranking per macromolecule; 4- averaging the ranking per macromolecule creating a final ranking. This last step incorporated the heterogeneity of the macromolecule conformations in the consensual score. The final ranking based on the adapted ECR represents relative affinity of a series of ligands to a macromolecule on average. As an example, a ranking of the average affinity of antidepressants and other ligands to the Drosophila melanogaster dopamine transporter (dDAT) was presented. Adapted ECR generated a ranking similar to that based on the affinity constant of each ligand obtained from the literature.• A final ranking of the average relative affinity of different ligands to the dDAT.• A consensus method combining multiple ensemble dockings.• A complete protocol to make re-docking and cross-docking using Autodock Vina, Gold and DockThor. |
| first_indexed | 2024-04-12T02:19:16Z |
| format | Article |
| id | doaj.art-b60089376698496ab24031a173b5931d |
| institution | Directory Open Access Journal |
| issn | 2215-0161 |
| language | English |
| last_indexed | 2024-04-12T02:19:16Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | MethodsX |
| spelling | doaj.art-b60089376698496ab24031a173b5931d2022-12-22T03:52:10ZengElsevierMethodsX2215-01612022-01-019101788Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexesFabiani Triches0Francieli Triches1Cilene Lino de Oliveira2Department of Physiological Sciences, Center of Biological Sciences, Federal University of Santa Catarina, University Campus, Trindade, Florianópolis, SC BrazilDepartment of Mathematics, Center of Physic and Mathematics, Federal University of Santa Catarina, University Campus, Trindade, Florianópolis, SC BrazilDepartment of Physiological Sciences, Center of Biological Sciences, Federal University of Santa Catarina, University Campus, Trindade, Florianópolis, SC BrazilDocking using different programs provides more reliable information about the interaction of molecules than data obtained in a single program. An exponential consensus ranking (ECR) was developed to combine scoring functions across docking programs differing in efficiencies and scales of measurements. The ECR method was adapted to merge results of re- and cross-dockings (i.e., ensemble docking) made in multiple docking programs. Adapted ECR consisted of four consecutive steps: 1- determination of scoring functions for a ligand with a series of macromolecules in multiple docking programs; 2- ranking of the scoring functions per macromolecule in each program; 3- combining the ranking across the programs creating a ranking per macromolecule; 4- averaging the ranking per macromolecule creating a final ranking. This last step incorporated the heterogeneity of the macromolecule conformations in the consensual score. The final ranking based on the adapted ECR represents relative affinity of a series of ligands to a macromolecule on average. As an example, a ranking of the average affinity of antidepressants and other ligands to the Drosophila melanogaster dopamine transporter (dDAT) was presented. Adapted ECR generated a ranking similar to that based on the affinity constant of each ligand obtained from the literature.• A final ranking of the average relative affinity of different ligands to the dDAT.• A consensus method combining multiple ensemble dockings.• A complete protocol to make re-docking and cross-docking using Autodock Vina, Gold and DockThor.http://www.sciencedirect.com/science/article/pii/S2215016122001686Autodock VinaConsensus dockingDockThorEnsemble dockingGoldMolecular docking |
| spellingShingle | Fabiani Triches Francieli Triches Cilene Lino de Oliveira Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes MethodsX Autodock Vina Consensus docking DockThor Ensemble docking Gold Molecular docking |
| title | Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes |
| title_full | Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes |
| title_fullStr | Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes |
| title_full_unstemmed | Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes |
| title_short | Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes |
| title_sort | consensus combining outcomes of multiple ensemble dockings examples using ddat crystalized complexes |
| topic | Autodock Vina Consensus docking DockThor Ensemble docking Gold Molecular docking |
| url | http://www.sciencedirect.com/science/article/pii/S2215016122001686 |
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