REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.

By A. Vagin, R. Steiner, A. Lebedev, Liz Potterton, S. McNicholas, F. Long, G. Murshudov. 2004

1,368 citations recorded by the source corpus.

One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Computational Chemistry & Drug Discovery

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “For bond lengths and angles, Phenix makes use of the CCP4 monomer library restraints (Engh & Huber, 1991; Vagin & Murshudov, 2004; Vagin et al., 2004) in protein side chains and somewhat modified classic values for nucleic acids (Clowney et al., 1996; Gelbin et al., 1996).”
Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “The second stage of the PDB interpretation involves matching the structural data with definitions in the CCP4 Monomer Library (Vagin & Murshudov, 2004; Vagin et al., 2004) in order to derive geometry restraints, scattering types and nonbonded energy types.”
Features and development of Coot (2010, neutral): “It also provides convenient interfaces to external validation tools: most notably the MolProbity suite (Davis et al. , 2007), but also to the REFMAC reﬁnement software (Murshudov et al. , 1997) and dictionary (Vagin et al. , 2004).”
Overview of the CCP4 suite and current developments (2011, methodology): “In REFMAC5 this is handled through a dictionary of possible ligands (Vagin et al., 2004), with details held in mmCIF format.”
Solving the scalability issue in quantum-based refinement: Q|R#1. (2017, background): “The currently used parameterized restraints (Engh & Huber, 1991; Grosse-Kunstleve et al., 2004; Vagin et al., 2004) are often insufficient to maintain (or obtain) an accurate atomic model (Zheng, Reimers et al., 2017).”
Human coronaviruses OC43 and HKU1 bind to 9-O-acetylated sialic acids via a conserved receptor-binding site in spike protein domain A (2019, methodology): “Vagin AA, et al. (2004) REFMAC5 dictionary: Organization of prior chemical knowl- edge and guidelines for its use.”
Modelling dynamics in protein crystal structures by ensemble refinement (2012, neutral): “To test the effect of the starting structure three datasets (1UOY, 3CA7 and 1BV1) were re-refined with Buster, phenix.refine and Refmac as given by the PDB_REDO server.”
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution (2012, positive): “In addition to the default restraints and the Ramachandran potentials, a fourth set of refinements were performed incorporating torsion restraints for the protein backbone using the uncoupled ’, values defined in the CCP4 monomer library (Vagin et al., 2004).”