[RASMB] SOMO: a new program for constructing hydrodynamic bead models

[Olwyn Byron]

Hi Everyone,

We'd like to draw your attention to the release 
of a new program for constructing hydrodynamic 
bead models. SOMO generates models from atomic 
coordinates (of proteins and carbohydrates) and 
retains the local characteristics of the 
macromolecule (i.e. beads correspond with amino 
acids etc). It also "intelligently" hydrates the 
model. Hydrodynamic parameters for SOMO models 
can then be computed either with José García de 
la Torre's group's program (HYDRO) or with Mattia 
Rocco's group's program (SUPC).

The program is described in the recent volume of Structure:

http://www.structure.org/

On a note of shameless self-publicity we'd like 
to advise you that our paper features on the 
cover of the journal.  We mention this because we 
feel it raises the profile of hydrodynamics in 
general and bead modelling in particular and that 
it may be of use to some of you in persuading 
funding agencies to support this aspect of your 
work.

Finally, we invite you to download the program from

http://malvinas.molgen.gla.ac.uk/~mrc/Public/somo_old/somo_home.htm

and to try it out.

We're very interested to hear from users and 
we're happy to advise on the use of SOMO in any 
way we can.  In addition we'd like to hear from 
you any comments you may have about the future of 
hydrodynamic modelling so that we can try to 
address them as we continue to develop SOMO.

With best wishes-

Mattia Rocco and Olwyn Byron

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