JLigand: a graphical tool for the CCP4 template-restraint library
- University of York, Heslington, York YO10 5DD (United Kingdom)
- University of Exeter, Stocker Road, Exeter EX4 4QD (United Kingdom)
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom)
The CCP4 template-restraint library defines restraints for biopolymers, their modifications and ligands that are used in macromolecular structure refinement. JLigand is a graphical editor for generating descriptions of new ligands and covalent linkages. Biological macromolecules are polymers and therefore the restraints for macromolecular refinement can be subdivided into two sets: restraints that are applied to atoms that all belong to the same monomer and restraints that are associated with the covalent bonds between monomers. The CCP4 template-restraint library contains three types of data entries defining template restraints: descriptions of monomers and their modifications, both used for intramonomer restraints, and descriptions of links for intermonomer restraints. The library provides generic descriptions of modifications and links for protein, DNA and RNA chains, and for some post-translational modifications including glycosylation. Structure-specific template restraints can be defined in a user’s additional restraint library. Here, JLigand, a new CCP4 graphical interface to LibCheck and REFMAC that has been developed to manage the user’s library and generate new monomer entries is described, as well as new entries for links and associated modifications.
- OSTI ID:
- 22347879
- Journal Information:
- Acta Crystallographica. Section D: Biological Crystallography, Vol. 68, Issue Pt 4; Other Information: PMCID: PMC3322602; PMID: 22505263; PUBLISHER-ID: dz5247; OAI: oai:pubmedcentral.nih.gov:3322602; Copyright (c) Lebedev et al. 2012; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449
- Country of Publication:
- Denmark
- Language:
- English
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