Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking

By Shengyou Huang, Xiaoqin Zou. 2006

373 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Organic Chemistry

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Citations in the corpus

MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15–19 (2010, methodology): “28,29 To validate the hierarchical protein docking algorithm (MDockPP) and the iterative knowledge-based scoring function (ITScorePP), we participated in the CAPRI (Critical Assessment of Prediction of Interactions) experiments — a community-wide blind test for protein-protein interactions,30–32…”
HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm (2018, methodology): “Recently, several global peptide docking algorithms such as AnchorDock (12), CABS-dock (10), pepATTRACT (8) and MDockPep (7) have been developed for the blind prediction of protein–peptide complexes, among which CABS-dock is available as a web server and pepATRRACT has a web version for its rigid do”
Advances and Challenges in Protein-Ligand Docking (2010, methodology): “Examples of docking programs that use shape matching include DOCK [1], FRED [44], FLOG [45], EUDOC [46], LigandFit [47], Surflex [48], MS-DOCK [49], and MDock [32,33].”
An iterative knowledge‐based scoring function for protein–protein recognition (2008, background): “35,73,74 On average, evaluating (including optimization) 2001 ligand orientations for a target using the atom-level scoring function, ITScore-PP, took about 1 min on a personal computer with 3.2 GHz Pentium IV CPU and 3.0 GB RAM.”
Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, methodology): “MDOCK was validated on 10 protein ensembles containing 104 crystal structures and 87 ligands, both in terms of binding mode and energy score predictions.”