Computer science Customizing scoring functions in molecular docking UNIVERSITY OF CALIFORNIASAN FRANCISCO Ajay N. Jain PhamTuan AnhIn 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 ...
5 Machine‑Learning‑Based Scoring Functions 5.1 support vector machine (SVM) 5.2 Random Forest (RF) 5.3 Artificial Neural Network (ANN) 5.4 Deep Learning (DL) 6 Conclusion Abstract 目前,分子对接已成为药物发现和分子建模应用中的关键工具。分子对接的可靠性取决于采用的打分函数的准确性,该函数可以在...
Molecule 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 gradually emerged as a promising alternative for protein–...
The proposed compact reformulation of the RRHO entropy term could constitute the basis for new and more effective scoring functions in molecular docking-based high-throughput virtual screening for drug discovery. © 2016 Wiley Periodicals, Inc.Piero Procacci...
Docking is generally devised as a multi-step process in which each step introduces one or more additional degrees of complexity. The process begins with the application of docking algorithms that pose small molecules in the active site. These algorithms are complemented by scoring functions that are...
In this benchmark test, 84% of the highest-scored docking conformations had root-mean-square deviations (rmsds) below 2.0 from the native conformation, which is comparable with the best of several energy-based docking scoring functions. Many of the top motifs, which comprise a multitude of ...
2.3.3. Evaluation of the Docking Power. “对接能力”是指打分函数从计算机生成的decoy中识别天然配体结合姿势的能力。理想情况下,天然结合姿势应被识别为排名第一的一个。如第2.2.2节所述,为每个蛋白质-配体复合物生成了包含最多100个配体结合姿势的decoy集。将天然配体结合姿势添加到相应的decoy集中以确保该集中...
Docking techniques are typically used to carry out this in silico prediction using their embedded scoring functions (SFs). When applied to VS, SFs seek to rank compounds based on their predicted affinity for the target as a way to discriminate between binders and non-binders. Despite the well-...
The results showed that the function successfully discriminates the incorrect docking predictions. In correctly predicted targets, the scoring function was complemented by other considerations, such as consistency of the oligomeric states among templates, similarity of the biological functions, biological ...
Seifert, M.H., Optimizing the signal-to-noise ratio of scoring functions for protein--ligand docking. J Chem Inf Model, 2008. 48(3): p. 602-12.Seifert MHJ: Optimizing the Signal-to-Noise Ratio of Scoring Functions for Protein-Ligand Docking. J Chem Inf Model 2008, 48 (3) : 602-...