Computational drug design accommodating receptor flexibility: the relaxed complex scheme.

By Jung-Hsin Lin, Alexander L. Perryman, Julie R. Schames, James Andrew McCammon. Journal of the American Chemical Society, 2002

380 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d5fdc554c33497d77037598a21b394a5800b61ff

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Citations in the corpus

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].”
Accounting for receptor flexibility and enhanced sampling methods in computer aided drug design (2013, methodology): “Other diketo acid HIV integrase inhibitors have been modeled and designed using RCS (30).”
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking (2006, background): “28,29 Kuhn and co-workers also developed a graph-theoretic algorithm to model protein main-chain flexibility.”
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, background): “…particular, McCammon et al. developed the so-called Relaxed-Complex Scheme (RCS), consisting in docking mini-libraries of compounds with AutoDock (Morris et al., 1998) against a large ensemble of snapshots derived from unliganded protein MD trajectories (Lin et al., 2002, 2003; Amaro et al., 2008).”
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility (2015, methodology): “…are deformed [12], or a consensus potential is created to represent various conformations of the receptor [13]; 2) ensemble docking methods [13, 14], using a discrete set of receptor conformations; and 3) induced fit methods, where changes in receptor conformation are explored during the…”
Molecular dynamics simulations and drug discovery (2011, methodology): “The successful applications of alchemical techniques in recent years are legion; accurate predictions have been obtained for ligand binding to the src SH2 domain [59], to a mutant T4 lysozyme [60], to FKBP12 [61], to HIV reverse transcriptase [62], to trypsin [63], to a bacterial ribosome [64], and ”
Using AutoDock for Ligand‐Receptor Docking (2008, methodology): “In the context of ﬂexible ligand-protein docking, McCammon and co-workers have introduced the relaxed complex method (Lin et al., 2002, 2003; McCammon, 2005), in which the ﬂexibility of the target is effectively pre-calculated using molecular dynamics calculations carried out on the apo form.”
Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, background): “Some different approaches have explored this basic idea [12, 60, 71-76], with alternatives differing on the sources employed to generate multiple protein structures (X-ray crystallographic structures, NMR, molecular dynamics, monte carlo simulations, or elastic network normal mode analysis technique”
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement (2012, methodology): “There are other methods that use calculated interaction energies (Goodford, 1985; Laurie and Jackson, 2005; Wade et al., 1993) or protein structure dynamics (Landon et al., 2008; Lin et al., 2002) to examine the click of ‘‘lock and key.’’”