Sir2019
Sir2019 is the updated version of Sir2014, a widely used software for the automatic solution of small, medium and large (proteins or nucleic acid) structures, using either X-ray or electron single-crystal diffraction data.
It includes different phasing algorithms and many new features described in the program help.
Among them:
Ab initio phasing approaches:
• Modern Direct Methods (MDM)
• Standard Direct Methods (SDM)
• Vive la Difference (VLD)
• Patterson pipeline (from the application of Patterson techniques to the Automated Model Building)
Non ab initio phasing approaches:
• Simulated Annealing (for s/m molecules)
• A new Molecular Replacement pipeline (from MR application to the Automated Model Building)
• A SAD/MAD pipeline (from SAD/MAD application to the Automated Model Building)
The program contains tools for crystal structure refinement and for the study of three-dimensional electron-density maps via the software JAV, a new integrated 3D visualizer.
RESEARCH AREA
KEYWORDS
Burla M.C., Caliandro R., Carrozzini B., Cascarano G.L., Cuocci C., Giacovazzo C., Mallamo M., Mazzone A, and Polidori G.
Crystal structure determination and refinement via SIR2014
J. Appl. Crystallog. (2015). 48, 306–309; doi:10.1107/S1600576715001132
Sir2014/19 was applied and cited in:
Yu Z., Wang H., Kong X. et al. “Molecular design for electrolyte solvents enabling energy-dense and long-cycling lithium metal batteries” (2020) Nat. Energy, 5, 526–533. doi:10.1038/s41560-020-0634-5
Zou Z., Habraken W.J.E.M., Matveeva G., Jensen A.C.S. et al. “A hydrated crystalline calcium carbonate phase: Calcium carbonate hemihydrate” (2019) Science, 363, 396-400. doi: 10.1126/science.aav0210. PMID: 30679371.
Shen Y., Mevius D.E.H.F. Caliandro R. et al. “Set7 Is a H3K37 Methyltransferase in Schizosaccharomyces pombe and Is Required for Proper Gametogenesis” (2019) Structure, 27, 631-638. doi:10.1016/j.str.2019.01.011
Mooers, B.H. “Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry” (2016) Acta Crystallogr. D72, 477-487. doi:10.1107/S2059798316001224
Venugopala K., Rao D., Bhandary S. et al. “Design, synthesis, and characterization of (1-(4-aryl)-1H-1,2,3-triazol-4-yl)methyl, substituted phenyl-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylates against Mycobacterium tuberculosis”. (2016) Drug Des. Devel. Ther., 10, 2681-2690. doi:10.2147/DDDT.S109760
