Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest
نویسندگان
چکیده
منابع مشابه
Development of target-biased scoring functions for protein-ligand docking
Accurate scoring of protein-ligand interactions for docking, binding-affinity prediction and virtual screening campaigns is still challenging. Despite great efforts, the performance of existing scoring functions strongly depends on the target structure under investigation. Recent developments in the direction of target-classspecific scoring methods and machine-learning-based procedures reveal s...
متن کاملAssessing scoring functions for protein-ligand interactions.
An assessment of nine scoring functions commonly applied in docking using a set of 189 protein-ligand complexes is presented. The scoring functions include the CHARMm potential, the scoring function DrugScore, the scoring function used in AutoDock, the three scoring functions implemented in DOCK, as well as three scoring functions implemented in the CScore module in SYBYL (PMF, Gold, ChemScore)...
متن کاملCombination of scoring functions improves discrimination in protein-protein docking.
Two structure-based potentials are used for both filtering (i.e., selecting a subset of conformations generated by rigid-body docking), and rescoring and ranking the selected conformations. ACP (atomic contact potential) is an atom-level extension of the Miyazawa-Jernigan potential parameterized on protein structures, whereas RPScore (residue pair potential score) is a residue-level potential, ...
متن کاملDistilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
For the successful identification and docking of new ligands to a protein target by virtual screening, the essential features of the protein and ligand surfaces must be captured and distilled in an efficient representation. Since the running time for docking increases exponentially with the number of points representing the protein and each ligand candidate, it is important to place these point...
متن کاملA Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions
A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate conformations mimicking the complex existing in vivo between two proteins, and a scoring function is used to rank them in order to extract a native-like one. We have already shown that using Voronoi constructions and a well chosen set of parameters, an acc...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2016
ISSN: 0192-8651
DOI: 10.1002/jcc.24667