Bioisis

Latest Reviews

27 February 2015  RECONSTRUCTION OF SAXS PROFILES FROM PROTEIN STRUCTURES

Excellent review on SAXS, this should be required reading material for anyone wanting to learn SAXS.

Comput Struct Biotechnol J. 2013; 8: e201308006

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Small angle X-ray scattering (SAXS) is used for low resolution structural characterization of proteins often in combination with other experimental techniques. After briefly reviewing the theory of SAXS we discuss computational methods based on 1) the Debye equation and 2) Spherical Harmonics to compute intensity profiles from a particular macromolecular structure. Further, we review how these formulas are parameterized for solvent density and hydration shell adjustment. Finally we introduce our solution to compute SAXS profiles utilizing GPU acceleration.


23 July 2013  ACA 2013 MONDAY SESSION

Greg Hura from SIBYLS beamline at ALS/LBNL talked about learning new biology with high-throughput SAXS by getting back to hypothesis testing and the scientific method. How? He described several applications of his new Volatility-of-ratio metric applied to comparison heatmaps, which SAXS users can access at http://bl1231.als.lbl.gov/saxs_similarity/. Michal Hammel from SIBYLS beamline presented a talk, “Prediction of Protein Crystallizibility from SAXS” aka “You Never Know.” Kratky plots and Porod exponents did not help him in these efforts. His main summary: the worst looking SAXS profiles may indicate crystallizable constructs. Bragg peaks (even at low concentrations) can indicate nucleation and be informative as to positioning within complexes. SAXS is a tool of comparison, but there is a high level of false positive/false negative. Philip Anfinrud brought up the notion of undoing the orientational averaging in SAXS by polarizing the system via illuminating a chromatically active protein coupled to 100 ps timeresolved SAXS.


21 July 2013  SEC SAXS IN AUSTRALIA

Kirby of the Australian beamline presented at ACA 2013 advances that allow them to measure less than 0.1 mg/mL using a size exclusion chromatography system attached to SAXS cell. The data was exception and opens up great opportunities for studying complexes by SAXS. They examined RIG-1 helicase with RNA and the SAXS data was modeled using MONSA, and atomistic modeling.


21 July 2013  ACA 2013 WORKSHOP

Awesome workshop for beginners and advanced users. Well organized and I have to thank Richard Gillian and Michal Hammel for their hard work and excellent planning. The speakers provided hands on working examples showing different applications of SAXS.

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15 July 2013  2013 ACA SAXS WORKSHOP

Bio-SAXS workshop at ACA 2013 in Hawaii. There will be two tracks: A) introduction to SAS and B) advanced SAXS analysis. The workshop will be all day and give hands on practical experience.

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