In drug discovery, where a model of the protein structure is known, molecular docking is a well-established approach for predictive modeling. Docking algorithms utilize a search strategy for exploring ligand poses within an active site and a scoring function for evaluating the poses. This ...
此外,可以使用新类型的特征(分子间特征、仅配体和仅蛋白质特征)来提高评分函数的性能,将这些评分函数作为开放软件生成对于这个领域的更多研究人员来说也非常重要。 Li, J., Fu, A. & Zhang, L. An Overview of Scoring Functions Used for Protein–Ligand Interactions in Molecular Docking.Interdiscip Sci Comput...
Automated docking is one of the most important tools for structure-based drug design that allows prediction of ligand binding poses and also provides an estimate of how well small molecules fit in the binding site of a protein. A new scoring function based on AutoDock and AutoDock Vina has ...
Molecular DockingMolecular Dynamics Simulation in Drug Design About this entry Cite this entry (2006). Scoring Function. In: Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine. Springer, Berlin, Heidelberg . https://doi.org/10.1007/3-540-29623-9_8634 Download citation .RIS .EN...
straightforwardly compute the absolute standard dissociation free energy without resorting to expensive normal mode analysis or other dynamical matrix-based techniques for evaluating the entropic contribution, hence providing an effective scoring function for assessing docking poses with no adjustable parameters...
Improving molecular docking through eHiTS' tunable scoring function – Supporting Materials Orr Ravitz*, Zsolt Zsoldos and Aniko Simon SimBioSys Inc. 135 Queen's Plate Dr. Unit 520, Toronto, Ontario M9W 6V1 Canada 416-741-4263 416-741-5084 ravitz@simbiosys.com http://www.simbiosys....
molecular dockingscoring functionstructure‐based drug designMolecule docking has been regarded as a routine tool for drug discovery, but its accuracy highly depends on the reliability of scoring functions (SFs). With the rapid development of machine learning (ML) techniques, ML‐based SFs have ...
Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions The scoring function is one of the most important components in structure-based drug design. Despite considerable success, accurate and rapid prediction of... Huang, Sheng-You,SZ Grinter,...
A function expressing the energy of a system as a sum of diverse molecular mechanics (or other) terms. TORSIONAL ENTROPY Entropy associated with a rotatable bond in a molecule. Immobilization of a rotatable bond on binding leads to loss of its torsional (or rotational) entropy. ...
Conversely, DNA–drug and RNA–drug dockings are generally less investigated. In particular, we did not find a QSBR scoring function for DNA–Furocoumarin docking. The furocoumarins are a class of natural or synthetic compounds with very interesting pharmacological properties [47], commonly used in...