[RASMB] RV: HYDROPRO, HYDRO++ : new versions

[Jose Garcia de la Torre]

Dear colleagues,

 

We are glad to announce versions  (#10) of programs HYDRO++ and HYDROPRO,
including graphical user interfaces (GUIs)  for both programs. As usual,
these software pieces can be freely downloaded from:

http://leonardo.inf.um.es/macromol/programs/programs.htm

 

[NOTE: because of some technical problems with the University network, the
link to the web site may temporarily fail. It may be wise to download the
software while it works properly.!]

 

Some advances that had been already included in a previous beta (testing)
version, HYDRO++ version 9beta, are now consolidated in version 10

 

Regarding HYDROPRO, there are important novelties regarding alternative ways
of modelling: 

(a)    at a residue level, with one element per residue, in addition to the
previous method that started from atomic-level models

(b)   making calculations directly from bead models, as an option
alternative to the previous shell modelling

and there is also a remarkable improvement in computational efficiency. 

 

All these advances are reported in our recent paper:

 

A. Ortega, D. Amoros, J. Garcia de la Torre, "Prediction of hydrodynamic and
other solution properties of rigid proteins from atomic- and residue- level
models", Biophysical Journal 101, 892-898 (2011) (see also accompanying
Supporting Material).

 

Thus, HYDROPRO calculation can be now done for arbitrarily large proteins
(as big as the 70 S ribosome), with atomic- or residue- level models, in
either console (batch) or GUI mode, with a computing time of about 10
seconds for shell model calculation (instead of 2 minutes, as required by
the previous version), or much less for residue-level bead model
calculations of small proteins. 

 

HYDRO++ also benefits from a great computational efficiency.

 

MS Windows and Linux executables are now available in our web site . The
GUIs work in Windows computers. Linux GUIs and Mac versions are to be
released a.s.a.p.

 

Our web site is being updated. In addition to structural and cosmetic
changes, new pieces of software - to be announced in another, forthcoming
message - will be released soon!.  Our group is glad to contribute with our
computer programs to the advance of so many fields in which macromolecular
hydrodynamics is involved, and we will welcome the feedback from users.

 

Jose Garcia de la Torre

 

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