Bioisis

Latest Journal Articles

04 September 2014  DENFERT: BEAD MODELING WITH HYDRATION

New dummy atom modeling algorithm that uses the Debye equation instead of spherical harmonic expansions. The algorithm attempts to model the hydration layer assuming a biphasic composition of the scattering volume.

J. Appl. Cryst. (2013). 46, 1884-1888
Incorporation of a hydration layer in the `dummy atom’ ab initio structural modelling of biological macromolecules

Link to Article
26 March 2013  IMPACT OF MACROMOLECULAR CROWDING ON DNA REPLICATION

Novel application of SAXS using changes in the radius-of-gyration as a function of crowding agent to follow the compaction of an enzyme (in this case the large DNA replication machinery). These types of SAXS studies can be applied to other systems and highlight the effects of modulating water activity on macromolecular structure.

Nat Commun. 2013 Mar 19;4:1615. Akabayov B, Akabayov SR, Lee SJ, Wagner G, Richardson CC.


15 January 2011  NOVEL 2-BODY COMPUTATIONAL APPROXIMATION FOR SAXS CALCULATIONS

Excellent computational approach for calculating SAXS profiles from proteins using a 2-body model per amino acid. The authors show, to high scattering angles, the new method is accurate and similar to CRYSOL.

Calculation of Accurate Small Angle X-ray Scattering Curves from Coarse-Grained Protein Models. BMC Bioinformatics. 2010; 11: 429. Stovgaard K, Andreetta C, Hamelryck T.

Link to Article
13 January 2011  A NEW APPROACH TO ENSEMBLE REFINEMENT OF SAXS DATA

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions. Structure. 2011 12;19(1):109-16. Rozycki B, Kim YC, and Hummer G.