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...
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 ...
If my own scoring function use a numpy array to represent the grids of molecules and proteins (the python function to turn them into grid has been completed) , and I need to use my own CNN scoring function model to instruct vina.dock(), I think there is no need to transfer the numpy...
Proteins: Structure, Function, and BioinformaticsChen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins. 2003;51(3):397-408.R. Chen and Z. Weng, "A novel shape complementarity scoring function for protein-protein docking," Proteins, vol. 51, no....
Scoring function is one of the most important components in molecular docking; it is used to predict the binding affinity between two molecules after they have been docked. Most of the scoring functions perform flexible ligand-rigid receptor docking, assuming that a receptor is a rigid object and...
Determination of parameter values for a chosen (linear or nonlinear) function to best fit a set of observations. POTENTIAL OF MEAN FORCE (PMF). In the context of docking and scoring, PMFs are derived from statistical analysis of experimentally observed distributions and frequencies of specific atom...
scoring 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 gradually emerged as...
A well studied problem in the area of Computational Molecular Biology is the so-called Protein-Protein Docking problem (PPD) that can be formulated as follows: Given two proteins A and B that form a protein complex, compute the 3D-structure of the protein complex AB. Protein docking algorithms...
This indicates that a necessary prerequisite to successfully resolving the scoring problem with a more discriminative scoring function is the generation of highly accurate ligand poses, which approximate the native pose to below 1 Å rmsd, in a docking run. 展开 ...
Modifications of the scoring function in FlexX for virtual screening applications A modification of the hydrogen bond score in the docking program FlexX is presented. Hydrogen bonds formed in inaccessibleregions of protein cavities there... Martin,Stahl - 《Perspectives in Drug Discovery & Design》 被...