ArticleBiophysics and physicobiology2016
Molecular dynamics analysis to evaluate docking pose prediction.
Article in Biophysics and physicobiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- Novel Thiourea and Oxime Ether Isosteviol-Based Anticoagulants: MD Simulation and ADMET Prediction.Pharmaceuticals (Basel, Switzerland) · 2024Article
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- Pharmacophore-Oriented Identification of Potential Leads as CCR5 Inhibitors to Block HIV Cellular Entry.International journal of molecular sciences · 2022Article
- In silico prediction, characterization, docking studies and molecular dynamics simulation of human p97 in complex with p37 cofactor.BMC molecular and cell biology · 2022Article
- Discovery of Rift Valley fever virus natural pan-inhibitors by targeting its multiple key proteins through computational approaches.Scientific reports · 2022Article
- Rational design and synthesis of modified natural peptides from Boana pulchella (anura) as acetylcholinesterase inhibitors and antioxidants.Amino acids · 2022Article
- A potential implication of UDP-glucuronosyltransferase 2B10 in the detoxification of drugs used in pediatric hematopoietic stem cell transplantation setting: an in silico investigation.BMC molecular and cell biology · 2022Article
- Main protease inhibitors and drug surface hotspots for the treatment of COVID-19: A drug repurposing and molecular docking approach.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2021Article
- Reversibly Sampling Conformations and Binding Modes Using Molecular Darting.Journal of chemical theory and computation · 2021Article
- Docking-generated multiple ligand poses for bootstrapping bioactivity classifying Machine Learning: Repurposing covalent inhibitors for COVID-19-related TMPRSS2 as case study.Computational and structural biotechnology journal · 2021Article
- Using yeast two-hybrid system and molecular dynamics simulation to detect venom protein-protein interactions.Current research in toxicology · 2021Article
- Prediction of potential inhibitors for RNA-dependent RNA polymerase of SARS-CoV-2 using comprehensive drug repurposing and molecular docking approach.International journal of biological macromolecules · 2020Article
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4 authors.
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Abstract
The accurate prediction of a ligand-protein complex structure is important for computer-assisted drug development. Although many docking methods have been developed over the last three decades, the success of binding structure prediction remains greatly limited. The purpose of this study was to demonstrate the usefulness of molecular dynamics (MD) simulation in assessing a docking pose predicted using a docking program. If the predicted pose is not unstable in an aqueous environment, MD simulation equilibrates the system and removes the ligand from the predicted position. Here we investigated two proteins that are important potential therapeutic targets: β2 adrenergic receptor (β2AR) and PR-Set7. While β2AR is rigid and its ligands are very similar to the template ligand (carazolol), PR-Set7 is very flexible and its ligands vary greatly from the template ligand (histone H4 tail peptide). On an empirical basis, we usually expect that the docking prediction is accurate when the protein is rigid and its ligands are similar to the template ligand. The MD analyses in this study clearly suggested such a tendency. Furthermore, we discuss the possibility that the MD simulation can predict the binding pose of a ligand.
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