ArticleJournal of computer-aided molecular design2015
Molecular dynamics to enhance structure-based virtual screening on cathepsin B.
Article in Journal of computer-aided molecular design, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed, 27 citations in OpenAlex.
- In Silico Study of Amylose Complexation with Quinoa (Chenopodium quinoa Willd.) Phenolic Compounds Under Different Temperatures.Plant foods for human nutrition (Dordrecht, Netherlands) · 2025Article
- Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.International journal of molecular sciences · 2024Article
- Identification of Potential p38γ Inhibitors via In Silico Screening, In Vitro Bioassay and Molecular Dynamics Simulation Studies.International journal of molecular sciences · 2023Article
- PyPLIF HIPPOS and Receptor Ensemble Docking Increase the Prediction Accuracy of the Structure-Based Virtual Screening Protocol Targeting Acetylcholinesterase.Molecules (Basel, Switzerland) · 2022Article
- Strategies to Control Human Health Risks Arising from Antibiotics in the Environment: Molecular Modification of QNs for Enhanced Plant-Microbial Synergistic Degradation.International journal of environmental research and public health · 2021Article
- Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures.Journal of chemical information and modeling · 2021Article
- Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations.Journal of chemical information and modeling · 2020Article
- Structure-Based Virtual Screening: From Classical to Artificial Intelligence.Frontiers in chemistry · 2020Review
- Docking Screens for Novel Ligands Conferring New Biology.Journal of medicinal chemistry · 2016Review
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) and molecular docking are commonly used to study molecular interactions in drug discovery. Most docking approaches consider proteins as rigid, which can decrease the accuracy of predicted docked poses. Therefore MD simulations can be used prior to docking to add flexibility to proteins. We evaluated the contribution of using MD together with docking in a docking study on human cathepsin B, a well-studied protein involved in numerous pathological processes. Using CHARMM biomolecular simulation program and AutoDock Vina molecular docking program, we found, that short MD simulations significantly improved molecular docking. Our results, expressed with the area under the receiver operating characteristic curves, show an increase in discriminatory power i.e. the ability to discriminate active from inactive compounds of molecular docking, when docking is performed to selected snapshots from MD simulations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.