Functionality maps of binding sites: A multiple copy simultaneous search method

By A. Miranker, Martin Karplus. 1991

Subfields: Computational Chemistry & Drug Discovery

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Citations in the corpus

The FTMap family of web servers for determining and characterizing ligand binding hot spots of proteins (2015, methodology): “Owing to this property, the FTMap results are essentially free of the many false-positive probe-binding positions predicted by classical methods such as GRID 38 or MCSS 39 (see also Mattos et al. 40 for a discussion of this issue).”
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites (2005, methodology): “of Miranker and Karplus (1991) has also been used to detect favourable binding sites for different functional groups.”
High-throughput crystallography for lead discovery in drug design (2002, methodology): “generates chemically reasonable structures from sp 3 CARBONS to fill the binding site, whereas the Multiple Copy Simultaneous Search (MCSS) metho”
Molecular docking: a powerful approach for structure-based drug discovery. (2011, methodology): “In addition to IC, Multiple Copy Simultaneous Search (MCSS) [55, 56] and LUDI [57] are fragment-based methods for the de novo design of ligands and modifications of known ligands that may enhance their binding to the target protein.”
A decade of fragment-based drug design: strategic advances and lessons learned (2007, background): “The fragmentation of drug leads into smaller pieces, or even into discrete functional groups (for example, carboxylate, amine, aryl group and so on), has been used for some time to simplify the computational analysis of ligand binding and to map out different pharmacophoric elements required for h”
Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, methodology): “Other less recent approaches such as AQUARIUS [103], CS-Map [104], MCSS [105], SuperStar [106] and most notably GRID[107] have also been described in the literature to identify potential water binding sites.”