FlexE: efficient molecular docking considering protein structure variations.

By Holger Claussen, Christian Buning, Matthias Rarey, T. Lengauer. Journal of Molecular Biology, 2001

446 citations recorded by the source corpus.

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

View Paper: https://www.semanticscholar.org/paper/667350a28fca989f86bf6a11c9a3da5d3fc970b8

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Citations in the corpus

Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, unknown): “FlexE Germany 2001 [149]”
Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations (2015, unknown): “Ensemble docking Already others have noted that docking against multiple receptor conformations (“ensemble docking”) can enhance performance relative to docking against a single static conformation (152-160).”
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go (2008, background): “…of the protein structure can reduce the impact of the induced fit upon binding, many other studies have shown the significant impact of protein flexibility on the docking accuracy (Clau (cid:1) en et al ., 2001; Carlson, 2002; Osterberg et al ., 2002; Zentgraf et al ., 2006; Corbeil et al ., 2007).”
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking (2006, methodology): “22 Claussen et al. have developed a new molecular docking tool FlexE to combine multiple protein structures to represent a flexible binding site.”
Molecular docking: a powerful approach for structure-based drug discovery. (2011, background): “Recently many efforts have been made to deal with the flexibility of the receptor [36-42], however, flexible receptor docking, especially backbone flexibility in receptors, still presents a major challenge for available docking methods.”
Computer-aided drug-discovery techniques that account for receptor flexibility. (2010, unknown): “Composite protein conformations are generated by mixing and matching the flexible regions from various experimental structures while maintaining the average structure of rigid regions, thus producing novel structures that may be pharmacologically relevant [39].”
Protein flexibility in ligand docking and virtual screening to protein kinases. (2004, background): “FlexE incorporates flexibility through discrete alternative conformations of varying parts of the protein taken from structures that have a very similar backbone trace, which are merged in a combinatorial way and considered directly during the rigid ligand docking.(21) The method is evaluated for ro”