Crystal structures

By Ram Seshadri. 2004

Subfields: Computational Chemistry & Drug Discovery, AI for Physical Sciences

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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…”
Protein sequence design with a learned potential (2022, neutral): “The high-resolution F2C structure was traced with Buccaneer 73 and went through manual ﬁ tting using COOT 74 and re ﬁ nement using REFMAC 75 .”
Polder maps: improving OMIT maps by excluding bulk solvent (2017, methodology): “The utility of OMIT maps may be limited by the flat bulksolvent model that is commonly used in macromolecular crystallographic packages such as CNS (Brünger et al., 1998), ISSN 2059-7983 REFMAC (Murshudov et al., 2011) and PHENIX (Adams et al., 2010).”
The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment – Olex2 dissected (2015, methodology): “The macromolecular community later introduced the limited-memory Broyden–Fletcher– Goldfarb–Shanno method (LBFGS, Nocedal, 1980), phenix.refine (Afonine et al., 2012) and a sparse Gauss–Newton algorithm, REFMAC (Murshudov et al., 2011, x4 and references therein).”
Structural and immunologic characterization of bovine, horse, and rabbit serum albumins (2012, methodology): “Refinement was done using HKL-3000 coupled with REFMAC5 (Murshudov et al., 2011), COOT (Emsley et al.”
AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. (2012, methodology): “For comparison, Rfree values were measured after SHELXE using REFMAC (Murshudov et al., 2011).”
Structural Changes Enable Start Codon Recognition by the Eukaryotic Translation Initiation Complex (2014, methodology): “Model building and refinement were carried out using Coot and Refmac (Murshudov et al., 2011) as recently described (Amunts et al.”
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps (2018, methodology): “Local refinement methods such as REFMAC (Murshudov et al., 2011), phenix.refine and phenix.real_space_refine (Afonine et al., 2012) perform far more local searches that aim to simultaneously optimize stereochemical restraints and fit to the data.”
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, methodology): “More recently, local NCS implementations in both REFMAC (Murshudov et al., 2011) and BUSTER (Smart et al., 2008, 2012) use local similarity restraints based on distances between atoms nearby in space.”
Exploiting sequence and stability information for directing nanobody stability engineering (2017, methodology): “Refmac [49] was used for structure refinement while model building of the two copies contained in the asymmetric unit was performed with coot [50].”
Recent developments in the CCP-EM software suite (2017, methodology): “REFMAC REFMAC has been used extensively for high-resolution structure refinement of macromolecules against X-ray crystallographic data (Murshudov et al., 2011).”