Refinement of macromolecular structures by the maximum-likelihood method.

By G. Murshudov, A. Vagin, E. Dodson. 1997

Subfields: Mathematical Optimization, Computational Biology & Bioinformatics

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Citations in the corpus

Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “By default, missing Fobs are ‘filled’ in with DFmodel [similar to the procedure used in the REFMAC program (Murshudov et al., 1997, 2011)], but there are other options possible, such as filling with hFobsi, where the Fobs are averaged out in a resolution bin around the missing Fobs, filling with…”
Features and development of Coot (2010, positive): “The geometry (bonds, angles, planes) for each residue in the selected molecule is compared with dictionary values (typically provided by the mmCIF REFMAC dictionary).”
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.”
Phaser crystallographic software (2007, methodology): “Rtm is a 1 n row vector of A values between the target and n models, which are approximated for each model using a four-parameter curve (Murshudov et al., 1997) tm ¼ fP 1 fsol exp Bsol 4d2 1=2 exp 2 2RMS2 3d2 ; ð19Þ where fP (= 1 by default) is the fraction of ordered structure modelled, fsol (=…”
BALBES: a molecular-replacement pipeline (2007, methodology): “Although the input is sufficiently simple, the output files contain all the process information, including the results of the analysis of the data by SFCHECK, REFMAC and MOLREP.”
Daedalus: a robust, turnkey platform for rapid production of decigram quantities of active recombinant proteins in human cell lines using novel lentiviral vectors (2011, unknown): “Model building and refinement were carried out using COOT (25) and refmac5 (26).”
Two Patched molecules engage distinct sites on Hedgehog yielding a signaling-competent complex (2018, methodology): “Human SHH-N (24-197) was constructed into pcDNA3.”
Crystal structure of chondroitin polymerase from Escherichia coli K4. (2009, methodology): “The structure was refined with the Refmac and CNS programs [14].”
Crystal Structures of Type-II Inositol Polyphosphate 5-Phosphatase INPP5B with Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights for the Inositol 5-Phosphatase Family (2016, unknown): “5 [24,28] (complex with BiPh(3,3,4,4,5,5)P6) or Buster 2.”