ArticleInternational journal of molecular sciences2014
Multipose binding in molecular docking.
Article in International journal of molecular sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Evaluating molecular docking for binding affinity predictions: a systematic analysis of key parameters and the utility of AlphaFold2 structures for the Schrödinger dataset.Journal of computer-aided molecular design · 2026Article
- Comparison of Protein-Glycosaminoglycan Interactions in ff14sb/GLYCAM06j-1 and CHARMM36m Force Fields.Journal of chemical information and modeling · 2026Article
- Machine learning models for prediction of (Pro)cathepsin-glycosaminoglycan binding free energies based on molecular structure.Computational and structural biotechnology journal · 2026Article
- Benchmark of Available Explicit Solvent Models in CHARMM36m to Characterize Glycosaminoglycans.The journal of physical chemistry. B · 2025Article
- Aptamers as Potential Inhibitors of Ethylene Biosynthesis: Identification and In Silico Selection.International journal of molecular sciences · 2025Article
- Analytical and biological assessment of Magnolia champaca L. stem bark: Integrating ATR-FTIR, GC-MS, thrombolytic activity, brine shrimp lethality and molecular docking.Journal, genetic engineering & biotechnology · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Density Functional Theory, Molecular Docking Study, andBiochemistry research international · 2025Article
- Article
- Spectroscopic and Molecular Docking Studies of the Interaction of Non-steroidal Anti-inflammatory Drugs with a Carrier Protein: an Interesting Case of Inner Filter Effect and Intensity Enhancement in Protein Fluorescence.Journal of fluorescence · 2024Article
- Revealing Molecular Mechanisms of the Bioactive Saponins from Edible Root ofPlants (Basel, Switzerland) · 2024Article
- Antifungal Constituents ofMolecules (Basel, Switzerland) · 2023Article
- Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin.Journal of chemical theory and computation · 2023Article
- Comprehensive chemical profiling of Bassia indica Wight. aerial parts extract using UPLC-ESI-MS/MS, and its antiparasitic activity in Trichinella spiralis infected mice: in silico supported in vivo study.BMC complementary medicine and therapies · 2023Article
- Detailed Experimental and In Silico Investigation of Indomethacin Binding with Human Serum Albumin Considering Primary and Secondary Binding Sites.Molecules (Basel, Switzerland) · 2023Article
- Spectroscopic and Molecular Docking Investigation on the Noncovalent Interaction of Lysozyme with Saffron Constituent "Safranal".ACS omega · 2020Article
- Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study.Journal of chemical information and modeling · 2020Article
- Molecular Modeling-Guided Design of Phospholipid-Based Prodrugs.International journal of molecular sciences · 2019Article
- Syntheses of defined sulfated oligohyaluronans reveal structural effects, diversity and thermodynamics of GAG-protein binding.Chemical science · 2019Article
- Synergistic Effects of Curcumin and Piperine as Potent Acetylcholine and Amyloidogenic Inhibitors With Significant Neuroprotective Activity in SH-SY5Y CellsFrontiers in aging neuroscience · 2019Article
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4 authors.
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Abstract
Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.
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