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The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures.

ABSTRACT: The protein databank now contains the structures of over 11,000 ligands bound to proteins. These structures are invaluable in applied areas such as structure-based drug design, but are also the substrate for understanding the energetics of intermolecular interactions with proteins. Despite their obvious importance, the careful analysis of ligands bound to protein structures lags behind the analysis of the protein structures themselves. We present an analysis of the geometry of ligands bound to proteins and highlight the role of small molecule crystal structures in enabling molecular modellers to critically evaluate a ligand model's quality and investigate protein-induced strain.

SUBMITTER: Liebeschuetz J

PROVIDER: S-EPMC3292722 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature

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The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures.

Liebeschuetz John J Hennemann Jana J Olsson Tjelvar T Groom Colin R CR

Journal of computer-aided molecular design 20120114 2

The protein databank now contains the structures of over 11,000 ligands bound to proteins. These structures are invaluable in applied areas such as structure-based drug design, but are also the substrate for understanding the energetics of intermolecular interactions with proteins. Despite their obvious importance, the careful analysis of ligands bound to protein structures lags behind the analysis of the protein structures themselves. We present an analysis of the geometry of ligands bound to p ...[more]

PMID: 22246295

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