Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

By G. Sastry, Matvey Adzhigirey, T. Day, R. Annabhimoju, Woody Sherman. Journal of Computer-Aided Molecular Design, 2013

5,465 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d6e1bd7af910a96502a9d62c04e696c6e635666c

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Citations in the corpus

Controlling the SARS-CoV-2 spike glycoprotein conformation (2020, positive): “Mutations at these sites were selected based upon in silico mutagenesis using the Schrödinger Biologics suite 16,17,18 .”
Best practices for constructing, preparing, and evaluating protein-ligand binding aﬃnity benchmarks [Article v0.2] (2021, methodology): “There are a number of tools to automate the steps described in this section, notably the Protein Preparation Wizard [116], the Molecular Operating Environment (MOE) [117], and Spruce [118].”
Sequence co-evolution gives 3D contacts and structures of protein complexes (2014, methodology): “Therefore, where possible we used complexes that had a solved 3D structure of the unbound monomer, namely GcsH/GcsT, CyoA, FimC, DhaL, AtpE, PtqA/PtqB, RS10 and HK/RR, and in all other cases the side chains of the monomers were randomized either by using SCWRL461 or restrained minimization with Schr”
Molecular dynamics simulation for all (2018, neutral): “Most of the common simulation software packages include some software for system preparation, and a number of recently introduced or improved software packages simplify the preparation process (Betz, 2017; Jo et al., 2008; Sastry et al., 2013).”
Using PyMOL as a platform for computational drug design (2017, methodology): “Ligand Preparation In structure-based protein–ligand modeling, all ligands must be well prepared with correct 3D geometries, proper bond orders, accessible tautomer, and proper ionization states prior to any other modeling tasks.(39,40) The Optimize plugin provides a PyMOL graphic interface to some ”
Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0] (2021, methodology): “There are a number of tools to automate the steps described in this section, notably the Protein Preparation Wizard [116], the Molecular Operating Environment (MOE) [117], and Spruce [118].”
Characterization and engineering of a plastic-degrading aromatic polyesterase (2018, background): “Additional details can be found in SI Appendix (62, 63).”