Likelihood-enhanced fast rotation functions.

By L. C. Storoni, A. McCoy, Randy J. Read. 2004

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Features and development of Coot (2010, positive): “Currently, suitable ﬁles are generated by the following software: Phaser (Storoni et al. , 2004), REFMAC (Murshudov et al. , 1997), phenix.reﬁne (Adams et al. , 2002), DM (Zhang et al. , 1997), Parrot (Cowtan, 2010), Pirate (Cowtan, 2000) and BUSTER (Blanc et al. , 2004).”
Phaser crystallographic software (2007, methodology): “A significant speed improvement is achieved in Phaser by the calculation of approximations to the Wilson MLRF0, the likelihoodenhanced fast rotation functions (LERFs; Storoni et al., 2004).”
BALBES: a molecular-replacement pipeline (2007, background): “All of these approaches are built around one or more of the popular molecular-replacement programs AMoRe (Navaza, 1987), MOLREP (Vagin & Teplyakov, 1997; Lebedev et al., 2008) and Phaser (Storoni et al., 2004).”
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…”
MUSTANG: A multiple structural alignment algorithm (2006, unknown): “Crystallographic packages such as PHASER [1, 2] can use ensembles of aligned structures as molecular replacement (MR) probes.”
Structural Characterization of the glycoprotein GP2 Core Domain from the CAS Virus, a Novel Arenavirus-like Species (2013, methodology): “The structure of pIICASV-GP2(267–351) was determined by molecular replacement with PHASER [49].”
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).”
Knowledge-based real-space explorations for low-resolution structure determination. (2006, methodology): “The model of the main structure was used as a molecular replacement probe in PHASER ( Storoni et al., 2004 ), along with two probes of the missing domains derived from the XRCC4 homolog consisting of just the secondary structural elements.”
Mechanism of activation and inhibition of the HER4/ErbB4 kinase. (2008, methodology): “The structures were determined by molecular replacement using the program PHASER (Storoni et al., 2004) and structures of the EGFR kinase domain with lapatinib (1XKK) and apo-EGFR kinase (1M14) as the search models, respectively.”
Crystal structures of the pilus retraction motor PilT suggest large domain movements and subunit cooperation drive motility. (2007, methodology): “The C2 PilT structure was solved by molecular replacement using the non-covalent CTDn:NTDn+1 domain pair from the refined PilT:ADP structure as the search model in PHASER (Storoni et al.).”
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).”
Recent developments in phasing and structure refinement for macromolecular crystallography (2009, background): “The introduction of likelihood targets [18–20] has increased the sensitivity of molecular replacement searches, thus allowing structures to be solved with more”