Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock

By F. Österberg, Garrett M. Morris, Michel F. Sanner, Arthur J. Olson, David S. Goodsell. Proteins: Structure, Function, and Bioinformatics, 2002

455 citations recorded by the source corpus.

Subfields: Infectious Diseases, Molecular Biology, Virology

View Paper: https://www.semanticscholar.org/paper/792a6cd059289448181ad3ab719126aa8d981f2f

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Citations in the corpus

Virtual ligand screening: strategies, perspectives and limitations (2006, background): “109 Österberg, F. et al. (2002) Automated docking to multiple target structures:”
Virtual Screening with AutoDock: Theory and Practice (2010, background): “Examples include energy-weighted averaging to model protein flexibility (described below) [22], covalent maps for prediction of covalently-linked complexes or metal coordination [1], mutable atom approaches for de novo design of ligands [23] and water maps for the prediction of bridging water positi”
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking (2006, methodology): “…methods, which combine different conformations into a single representation of an average energy grid and thus may lead to loss of geometric accuracy, 20,22,25 our ensemble docking algorithm treats each conformation of the ensemble separately during the energy calculations and pose optimization.”
GEMDOCK: A generic evolutionary method for molecular docking (2004, methodology): “48 Two ensembles of protein structures were used, namely, 8 complexes of the HIV-1 protease 23 and 5 complexes of the Fab’ fragment protein of monoclonal antibody DB3.”
Software for molecular docking: a review (2017, methodology): “structurally known protein–ligand complexes with experimentally determined binding constants (Österberg et al. 2002; Trott and Olson 2010).”
Protein–ligand docking: Current status and future challenges (2006, background): “Osterberg et al.(36) have addressed the protein flexibility”
Computer-aided drug-discovery techniques that account for receptor flexibility. (2010, unknown): “Candidate ligands are then docked into this ensembleaverage energy grid [43,44].”
A model binding site for testing scoring functions in molecular docking. (2002, background): “How to model such ordered water molecules in docking remains a matter for future study.(23,41,42) We only note here that neglecting it neither prevented us from finding novel ligands nor predicting their binding geometry.”
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go (2008, background): “…more than one protein conformations can be either combined leading to one (for example, DOCK; Knegtel et al ., 1997) or to a set of individual grids (for example, AutoDock; Osterberg et al ., 2002) or aligned into a larger grid modelling the conformational ensemble (Sotriffer and Dramburg, 2005).”