Novel procedure for modeling ligand/receptor induced fit effects.

By Woody Sherman, T. Day, Matthew P. Jacobson, Richard A. Friesner, R. Farid. 2006

1,930 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Organic Chemistry

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In Computational Theory and Mathematics

In Organic Chemistry

Citations in the corpus

Virtual screening strategies in drug discovery: a critical review. (2013, methodology): “Several docking programs including AUTODOCK4 [49], DOCK [50], GOLD [53], EADock [54], IFREDA [56], FlexE [90], or GLIDE induced Fit [91] (Table 7) allow rotation around torsional degrees of freedom of selected side”
Accounting for receptor flexibility and enhanced sampling methods in computer aided drug design (2013, methodology): “and implemented in the popular Schrödinger suite of tools as an option in the GLIDE docking program (19,20).”
Advances and Challenges in Protein-Ligand Docking (2010, methodology): “simulations, Monte Carlo simulations, or structure prediction have also been used to account for protein flexibility [35–43].”
Lifting the lid on GPCRs: the role of extracellular loops (2011, background): “Efforts have also been made to incorporate flexibility to mimic the effects of ‘induced-fit’ (Sherman et al., 2006; Michino et al., 2009).”
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get” (2009, neutral): “The drawbacks of MM-PBSA/GBSA are that it, too, is sometimes not predictive (Pearlman, 2005; Shirts et al., 2009; Steinbrecher et al., 2006) and it requires prior knowledge of a likely bound complex as a starting point, although such starting conformations can be taken from prior docking…”
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking (2006, background): “The idea can also be applied to improve the efficiency of a recently proposed new protocol for modeling ligand/receptor induced fit effect.(8) In this protocol, the ligand conformations and receptor conformations are sampled separately.”
Molecular docking: a powerful approach for structure-based drug discovery. (2011, methodology): “Then a rotamer exploration is used to further model receptor flexibility [36].”
Characterization and engineering of a plastic-degrading aromatic polyesterase (2018, background): “Additional details can be found in SI Appendix (62, 63).”