[RASMB] New HYDRO software: Erratum(1)

Mon Mar 26 04:15:18 PDT 2012

This is to correct an erratum in my previous message about the new
hydrodynamics programs MONTEHYDRO and SIMUFLEX. The link to the place where
they are temporarily deposited is

http://leonardo.inf.um.es/macromol/newprograms/

With my apologies, and best regards,
Jose Garcia de la Torre

-----Mensaje original-----
De: rasmb-bounces at rasmb.bbri.org [mailto:rasmb-bounces at rasmb.bbri.org] En
nombre de Jose Garcia de la Torre
Enviado el: domingo, 25 de marzo de 2012 14:15
Para: RASMB at rasmb.bbri.org
Asunto: [RASMB] HYDRO Suite: new hydrodynamics software

23/03/2012

Dear colleagues,

I am glad to announce new programs that, as the previous ones, can be  
freely downloaded from our repository.

After the previous release of programs for rigid biomacromolecules  
(announcement of  September 2011, reproduced below), we now provide  
new tools, mainly intended for the treatment of flexible entities

A few months ago we released  a new version of our MULTIHYDFIT  
program, which is intented for the joint analysis of several  
differente properties of a set of samples, in the search for  
structural parameters. In a recent paper (Macromolecules 2011, 44,  
5788-5897), we published a computational procedure that enables the  
calculation of properties of the wormlike chain model in the whole  
range that it covers, from short. thick rods to very long and flexible  
chains. This procedure has been implemented in the MULTIHYDIT toolkit,  
which remarkable successes, like the description of properties of DNA  
from 8 to 200 000 (T2 DNA) base pairs with very accurate values of the  
structural parameters of the double helix. The program is available from

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

In addition, we have further developed our tools for simulation of  
arbitrarily complex flexible particles. Thus, we have just released:

** New versions of the SIMUFLEX package (BROWFLEX and ANAFLEX) for the  
simulation of Brownian dynamics trajectories of models for particles  
with some extent and various types of flexibility

**New version of the MONTEHYDRO program, for MonteCarlo simulation of  
conformational and overall hydrodynamic properties.

These new versions of SIMUFLEX and MONTEHYDRO contain important  
improvements like:

a) New torsional and non-bonded interactions embodied in the force  
field, which enable the simulation of quite realistic models

b) Substantial improvements in computational efficiency, achieved by  
extensive use of parallelization in numerical calculation. This  
results in a great speed-up of the calculations in present multi-core  
processor, which can be, for instance, over ten-fold in a simple PC  
with Quad processor.

The present release is of these two packages is provisional, intended  
to have it announced for the 20th International AUC Conference, March  
2012, conference in San Antonio, Texas, USA. As the release packages  
have been prepared quite quickly, they may need some touches. Then,  
they are not placed in the our general software page, but instead yo  
can find them in a provisional location:

(NOW CORRECTED: http://leonardo.inf.um.es/macromol/newprograms/)

Final, definitive versions will be in available, from the general  
software page,  hopefully in April.

I hope these tools will be useful, and I will welcome comments,  
suggestions, bug reports, etc. which would help further developments.

José García de la Torre

***************************************************************

Announcement of a previous release, 21/09/2011

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

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