ArticleJournal of chemical information and modeling2018
Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking.
Article in Journal of chemical information and modeling, 2018. 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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- GPU-Accelerated Virtual Screening and Molecular Dynamics Simulations for Identification of Novel DPP‑4 Inhibitors.ACS omega · 2026Article
- Coumarin-Augmented Thiazole Hybrids as Dual Anticancer and Antibacterial Agents.Chemical biology & drug design · 2026Article
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- Integrative and Emerging Models in Antibody Research: A Comprehensive Review.Antibody therapeutics · 2025Review
- Trimetazidine-Profen Hybrid Molecules: Synthesis, Chemical Characterization, and Biological Evaluation of Their Racemates.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Multi-Component Synthesis of New Fluorinated-Pyrrolo[3,4-International journal of molecular sciences · 2025Article
- Molecular Docking in Drug Discovery: Techniques, Applications, and Advancements.Current medicinal chemistry · 2025Review
- Synthesis of Novel Benzothiazole-Profen Hybrid Amides as Potential NSAID Candidates.Molecules (Basel, Switzerland) · 2024Article
- In Vitro and Computational Response of Differential Catalysis byInternational journal of molecular sciences · 2024Article
- Synthesis, In Vivo Anticonvulsant Activity Evaluation and In Silico Studies of Some Quinazolin-4(3H)-One Derivatives.Molecules (Basel, Switzerland) · 2024Article
- Synthetic Glycans Reveal Determinants of Antibody Functional Efficacy against a Fungal Pathogen.ACS infectious diseases · 2024Article
- Novel Flurbiprofen Derivatives as Antioxidant and Anti-Inflammatory Agents: Synthesis, In Silico, and In Vitro Biological Evaluation.Molecules (Basel, Switzerland) · 2024Article
- A quinolin-8-ol sub-millimolar inhibitor of UGGT, the ER glycoprotein folding quality control checkpoint.iScience · 2023Article
- Exploring Pyrrolo-Fused Heterocycles as Promising Anticancer Agents: An Integrated Synthetic, Biological, and Computational Approach.Pharmaceuticals (Basel, Switzerland) · 2023Article
- In-vitro biological evaluation of 3,3',5,5'-tetramethoxy-biphenyl-4,4'-diol and molecular docking studies on trypanothione reductase and Gp63 from Leishmania amazonensis demonstrated anti-leishmania potential.Scientific reports · 2023Article
- Article
- PacDOCK: A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results.Molecules (Basel, Switzerland) · 2022Article
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Authors and funding
3 authors.
Funding
Abstract
In this work, we developed a computational protocol that employs multiple molecular docking experiments, followed by pose clustering, molecular dynamic simulations (10 ns), and energy rescoring to produce reliable 3D models of antibody-carbohydrate complexes. The protocol was applied to 10 antibody-carbohydrate co-complexes and three unliganded (apo) antibodies. Pose clustering significantly reduced the number of potential poses. For each system, 15 or fewer clusters out of 100 initial poses were generated and chosen for further analysis. Molecular dynamics (MD) simulations allowed the docked poses to either converge or disperse, and rescoring increased the likelihood that the best-ranked pose was an acceptable pose. This approach is amenable to automation and can be a valuable aid in determining the structure of antibody-carbohydrate complexes provided there is no major side chain rearrangement or backbone conformational change in the H3 loop of the CDR regions. Further, the basic protocol of docking a small ligand to a known binding site, clustering the results, and performing MD with a suitable force field is applicable to any protein ligand system.
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