[RASMB] US-SOMO updated version available

[Emre Brookes]

Dear RASMB members,


A major update US-SOMO has been released. This update focuses on 
improvements to hydrodynamic calculations.


The Generalized Rotne-Prager-Yamakawa (GRPY) method (Zuk et al. Biophys. 
J. 115:782-800, 2018) has been integrated. This method allows the 
computation of all the hydrodynamic parameters (translational diffusion 
and sedimentation coefficients, relaxation time, intrinsic viscosity) 
with high accuracy for models that can have overlapping beads of 
different sizes. It is, however, computationally intensive, limiting its 
application when large structures are studied, for which the ZENO method 
is a viable option if calculation of rotational diffusion is not 
required. A parallel version of GRPY will be included in a future release.


Additional features:

Upon loading a PDB structure, a search for disulfide-bonded and free 
cysteines is performed, enabling discrimination between the molecular 
properties of cystine versus cysteine when beads are generated and 
parameters such as the partial specific volume are computed. While this 
information can be already present in the PDB “SSBOND” field(s), this is 
not always the case.

The temperature and the pH at which the experimental data were collected 
can now be entered. The latter, coupled with information of the pK of 
ionizable residues now present in the somo.residue file, controls the 
ionization state of atoms, resulting in a more sound evaluation of the 
molecular weight, and of hydration, the latter an important parameter in 
the generation of appropriate bead models. Changes were made in the 
somo.residue editor to deal with this new feature.


Numerous other enhancements and bug fixes have been included. Some of 
these enhancements are described in the 2021 Edition of Encyclopedia of 
Biophysics Chapter entitled "US-SOMO: Methods for Construction and 
Hydration of Macromolecular Hydrodynamic Models" available at 
https://link.springer.com/referenceworkentry/10.1007/978-3-642-35943-9_292-1. 
The changes are also described and documented in the various Help pages 
included with US-SOMO and available online.


Get the latest information and download instructions at 
https://somo.aucsolutions.com


Best regards,

Emre Brookes emre.brookes at umontana.edu <mailto:emre.brookes at umontana.edu>

Mattia Rocco mattia.rocco at quipo.it <mailto:mattia.rocco at quipo.it>(please 
note new email !)
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