ArticleJournal of computer-aided molecular design2018
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.
Article in Journal of computer-aided molecular design, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
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- Open-ComBind: harnessing unlabeled data for improved binding pose prediction.Journal of computer-aided molecular design · 2023Article
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- Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics.International journal of molecular sciences · 2023Review
- Structure-based approach: molecular insight of pyranocumarins against α-glucosidase through computational studies.RSC advances · 2023Article
- Synergistic interactions of repurposed drugs that inhibit Nsp1, a major virulence factor for COVID-19.Scientific reports · 2022Article
- Effect ofJournal of diabetes and metabolic disorders · 2021Article
- Further exploration of the structure-activity relationship of dual soluble epoxide hydrolase/fatty acid amide hydrolase inhibitors.Bioorganic & medicinal chemistry · 2021Article
- Ligand Strain Energy in Large Library Docking.Journal of chemical information and modeling · 2021Article
- Structural Insights and Docking Analysis of Adamantane-Linked 1,2,4-Triazole Derivatives as Potential 11β-HSD1 Inhibitors.Molecules (Basel, Switzerland) · 2021Article
- Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20.Journal of chemical theory and computation · 2021Article
- Molecular docking studies, in-silico ADMET predictions and synthesis of novel PEGA-nucleosides as antimicrobial agents targeting class B1 metallo-β-lactamases.In silico pharmacology · 2021Article
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- Alkylated benzimidazoles: Design, synthesis, docking, DFT analysis, ADMET property, molecular dynamics and activity against HIV and YFV.Computational biology and chemistry · 2020Article
- Targeting the C-Terminal Domain Small Phosphatase 1.Life (Basel, Switzerland) · 2020Review
- Synergistic Effect of Chlorogenic Acid and Caffeic Acid with Fosfomycin on Growth Inhibition of a ResistantACS omega · 2020Article
- Review
- D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.Journal of computer-aided molecular design · 2020Article
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3 authors.
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Abstract
Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.
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