An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function

By Shengyou Huang, Xiaoqin Zou. 2006

152 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Computational Chemistry & Drug Discovery

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Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, methodology): “The method uses pairwise energy potentials extracted from known ligand-receptor complexes to obtain a general function [61].”
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking (2006, methodology): “36,37 Therefore, for each ligand, the energy score from native-docking was used as a reference to evaluate the energy scores obtained from cross docking.”
MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15–19 (2010, background): “34,35 The specific iterative equation is expressed as Here, k stands for the iterative step. i and j represent the types of a pair of atoms in the receptor and the ligand. g ij obs ( r ) is the pair distribution function for atom pair ij observed in the experimentally determined (i.e., native)…”
Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, methodology): “These approaches are used by ZDOCK [161], MDock [162,163], older versions of DOCK [164], et al. Actually, so-called rigid-body algorithms still consider the ligand flexibility by pre-computing ensembles of putative ligand conformations, followed by rigidly docking each conformation to the protein re”
Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, methodology): “The program uses an iterative knowledge-based scoring function [200, 201] called ITScore that includes only intermolecular interactions.”
Advances and Challenges in Protein-Ligand Docking (2010, methodology): “Huang and Zou have developed a physics-based iterative method and derived the ITScore scoring function, which has been extensively tested with multiple benchmarks for binding mode prediction, affinity prediction and virtual screening [136,137,148].”
An iterative knowledge‐based scoring function for protein–protein recognition (2008, methodology): “60,61 To extend the iterative approach from protein–ligand to protein–protein structure prediction, in this work we have derived an efficient energy scoring function for protein–protein interactions using the similar iterative procedure.60 An advantage of protein–protein systems over protein–ligand…”