Electronic Reprint Biological Crystallography Likelihood-enhanced Fast Translation Functions Biological Crystallography Likelihood-enhanced Fast Translation Functions

By A. McCoy, R. Grosse-Kunstleve, L. C. Storoni, Randy J. Read

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Citations in the corpus

• Phaser crystallographic software (2007, methodology): “As are the maximum likelihood rotation functions, the MLTF is slow to compute.”
• Rules for nuclear localization sequence recognition by karyopherin beta 2. (2006, unknown): “The partial SAD-phased model was used as a search model for molecular replacement using the program Phaser with the higher-resolution native dataset (McCoy et al., 2005).”
• MUSTANG-MR Structural Sieving Server: Applications in Protein Structural Analysis and Crystallography (2010, methodology): “identified a range of AhpD-like homologues with sequence identities between 16–20%. ‘Mixed’ models of the top six hits (non-conserved residues converted to alanines) were used in addition to testing a range (0.8 to 2.6 A) of RMSD inputs within PHASER”
• AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. (2012, methodology): “…the N-terminus to the C-terminus) is almost complete and very largely correct compared with the deposited crystal structure (grey). distributed in CCP4 v.6.3.0 is required) and MR was carried out by both Phaser (Storoni et al., 2004; McCoy et al., 2005, 2007) and MOLREP (Vagin & Teplyakov, 2010).”
• On the application of the expected log-likelihood gain to decision making in molecular replacement (2018, methodology): “The BETA–BLIP structure (Strynadka et al., 1996), which has previously been used as a test case for Phaser (Storoni et al., 2004; McCoy et al., 2005; McCoy, 2007), was used to generate simulated data with different hemihedral twin fractions, and the LLGI was calculated for the structure given the…”
• Phaser.MRage: automated molecular replacement (2013, background): “From the second molecule onwards, all 13 models yielded clear solutions with high Z-scores.”
• Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. (2016, methodology): “For example, Read and coworkers incorporated the use of maximum-likelihood statistics to enhance the sensitivity of MR searches (Read, 2001; Storoni et al., 2004; McCoy et al., 2005).”
• Molecular basis of AKAP specificity for PKA regulatory subunits. (2006, methodology): “The structure was solved by molecular re - placement with PHASER ( McCoy et al .”