دورية أكاديمية
Accurate prediction of dynamic protein-ligand binding using P-score ranking.
| العنوان: | Accurate prediction of dynamic protein-ligand binding using P-score ranking. |
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| المؤلفون: | Ibrahim PEGF; Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK., Zuccotto F; Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK., Zachariae U; Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK., Gilbert I; Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK., Bodkin M; Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK. |
| المصدر: | Journal of computational chemistry [J Comput Chem] 2024 Jul 30; Vol. 45 (20), pp. 1762-1778. Date of Electronic Publication: 2024 Apr 22. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Wiley Country of Publication: United States NLM ID: 9878362 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1096-987X (Electronic) Linking ISSN: 01928651 NLM ISO Abbreviation: J Comput Chem Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: New York : Wiley, |
| مواضيع طبية MeSH: | Proteins*/chemistry , Proteins*/metabolism , Molecular Dynamics Simulation* , Protein Binding*, Ligands ; Binding Sites ; Quantum Theory ; Thermodynamics |
| مستخلص: | Protein-ligand binding prediction typically relies on docking methodologies and associated scoring functions to propose the binding mode of a ligand in a biological target. Significant challenges are associated with this approach, including the flexibility of the protein-ligand system, solvent-mediated interactions, and associated entropy changes. In addition, scoring functions are only weakly accurate due to the short time required for calculating enthalpic and entropic binding interactions. The workflow described here attempts to address these limitations by combining supervised molecular dynamics with dynamical averaging quantum mechanics fragment molecular orbital. This combination significantly increased the ability to predict the experimental binding structure of protein-ligand complexes independent from the starting position of the ligands or the binding site conformation. We found that the predictive power could be enhanced by combining the residence time and interaction energies as descriptors in a novel scoring function named the P-score. This is illustrated using six different protein-ligand targets as case studies. (© 2024 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC.) |
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| معلومات مُعتمدة: | Welcome Centre for Anti-Infectives Research |
| فهرسة مساهمة: | Keywords: P‐score; binding pose prediction; dynamic average quantum mechanics fragment molecular orbital; supervised molecular dynamics |
| المشرفين على المادة: | 0 (Ligands) 0 (Proteins) |
| تواريخ الأحداث: | Date Created: 20240422 Date Completed: 20240612 Latest Revision: 20240612 |
| رمز التحديث: | 20240612 |
| DOI: | 10.1002/jcc.27370 |
| PMID: | 38647338 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1096-987X |
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| DOI: | 10.1002/jcc.27370 |