[RASMB] Characterizing Protein-Protein Interactions via Static and Dynamic Light Scattering

Sun Mar 25 12:44:11 PDT 2012

Dear Colleagues,

I am pleased to announce the recent publication of the open-access book Protein Interactions, ed. J. Cai and R.E. Wang, InTech 2012. The book is available for chapter-by-chapter download at 

http://www.intechopen.com/books/protein-interactions. 

The ook includes several chapters discussing characterization techniques. You may be particularly interested in Chapter 20, "Characterizing Protein-Protein Interactions via Static and Dynamic Light Scattering" co-authored by Sophia Kenrick and myself, freely downloadable at

http://www.intechopen.com/books/protein-interactions/characterization-of-protein-protein-interactions-via-static-and-dynamic-light-scattering.

Hope you find it interesting and useful!

with best regards,
Dan Some
e-mail: dsome at wyatt.com
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Today's Topics:

   1. HYDRO Suite: new hydrodynamics software (Jose Garcia de la Torre)

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Message: 1
Date: Sun, 25 Mar 2012 14:15:07 +0200
From: Jose Garcia de la Torre <jgt at um.es>
To: RASMB at rasmb.bbri.org
Subject: [RASMB] HYDRO Suite: new hydrodynamics software
Message-ID: <20120325141507.11036793hq8osguj at webmail.atica.um.es>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
        format="flowed"

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:

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

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.

Jos? Garc?a 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

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