Team, Visitors, External Collaborators
Overall Objectives
Research Program
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
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Section: New Software and Platforms


Keywords: Bioinformatics - Structural Biology - Data modeling

Functional Description: Pepsi-SAXS (PEPSI stands for Polynomial Expansions of Protein Structures and Interactions) is new implementation of the multipole-based scheme initially proposed by Stuhrmann (Stuhrmann, 1970). Overall, our method is significantly faster with a similar accuracy compared to Crysol, FoXS, and the 3D-Zernike implementation from the SAStbx package.

Release Functional Description: Version 1.0 from 6th March 2018: Added computation of P(r). Version 1.1 from 19th April 2018: Excluded solvent radii updated. Many more ions added. Version 1.2 from 24th April 2018: Added automatic identification of labile and nonlabile explicit hydrogens. Added bulk SLD option. Version 1.3 from 30th July 2018: Added initial prototype of 2D dcattering images. Version 1.4 from 1st August 2018: Added docking module. Version 2.0 from January 2019: Added flexible optimization of conformations. A bug with absolute contrast fixed. Default behaiviour of Pepsi-SAXS changed, now it reads all the hydrogen atoms if the –hyd flag is set. Otherwise, it reads only explicit hydrogens on non-standard residues. Version 2.1 from February 2019: First implimentation of the multi-structure fitting.