Molecular replacement with MOLREP.

By A. Vagin, A. Teplyakov. 2010

3,300 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy, Computational Biology & Bioinformatics, Computational Chemistry & Drug Discovery

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Citations in the corpus

Assessment of three-dimensional RNA structure prediction in CASP15 (2023, positive): “A portion comprising nucleotides 1 – 24;125 – 157 could then be placed with MOLREP which indicated a partial solution after FIGURE 9 Molecular replacement (MR) of x-ray crystallographic data using CASP15 models (and AlphaFold 2 models of U1ABD in the cases of R1107 and R1108).”
I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation (2017, methodology): “However, since different MR programs are often complementary, the success rate of I-TASSER-MR can be further improved by combining MR-REX with other state of the art phasing tools such as Phaser (20), Molrep (21) and AMoRe (22).”
Improvement of molecular-replacement models with Sculptor (2011, methodology): “These algorithms have since been implemented in the CCP4 (Winn et al., 2011) programs CHAINSAW (Stein, 2008) and MOLREP (Vagin & Teplyakov, 2010).”
Overview of the CCP4 suite and current developments (2011, methodology): “BALBES is based around the MR program MOLREP (Vagin & Teplyakov, 1997, 2010), while MrBUMP can also use the program Phaser (McCoy et al., 2007).”
Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, background): “…one needs to solve the ‘phase problem’ either by using prior knowledge about a related structure, i.e. molecular replacement (McCoy et al., 2007; Vagin & Teplyakov, 2010), or by carrying out additional experiments and determining phases for a substructure (SAD, MAD, SIR etc.; Sheldrick, 2015;…”
Recognition of cellooligosaccharides by a family 28 carbohydrate‐binding module (2010, methodology): “[11] Vagin, A. and Teplyakov, A. (2010) Molecular replacement with MOLREP.”
Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data (2019, background): “However, if the first operation for map interpretation is to fit the structure of a homolog or a previously obtained model into the map of interest, one would have no need for de novo tracing—just as, in MX, one would not first try to solve a structure with heavy atom derivatives if molecular replac”
Phaser.MRage: automated molecular replacement (2013, background): “Both BALBES and MrBUMP delegate molecular replacement to the underlying Phaser (McCoy et al., 2007) and/or MOLREP (Vagin & Teplyakov, 2010) binaries.”
Phosphorylation of p62 activates the Keap1-Nrf2 pathway during selective autophagy. (2013, positive): “Molecular replacement was performed using MOLREP (Vagin and Teplyakov, 2010).”
Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses (2021, methodology): “A data set from a single crystal was collected at Diamond Light Source (Didcot, UK) at a wavelength of 0.92819 Å. Data were processed using XDS [86] (S1 Table), and the structure was solved using molecular replacement with the program MOLREP [87] and available structures of DDB1 (PDB 3e0c) and DCAF1”