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<div class=Section1>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>Dear colleagues,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>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:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><a
href="http://leonardo.inf.um.es/macromol/programs/programs.htm">http://leonardo.inf.um.es/macromol/programs/programs.htm</a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>[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…!]<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>Some advances that had been already included in a <font
color=navy><span style='color:navy'>previous </span></font>beta (testing)
version, HYDRO++ version 9beta, are now consolidated in version 10<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>Regarding HYDROPRO, there are important novelties
regarding alternative ways of modelling: <o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><font
size=3 face="Times New Roman"><span lang=EN-GB style='font-size:12.0pt'><span
style='mso-list:Ignore'>(a)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><span
lang=EN-GB>at a residue level, with one element per residue, in addition to the
previous method that started from atomic-level models<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><font
size=3 face="Times New Roman"><span lang=EN-GB style='font-size:12.0pt'><span
style='mso-list:Ignore'>(b)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><span
lang=EN-GB>making calculations directly from bead models, as an option
alternative to the previous shell modelling<o:p></o:p></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>and there is also a remarkable improvement in computational
efficiency. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>All these advances are reported in our recent paper:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>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).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>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. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>HYDRO++ also benefits from a great computational efficiency.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>Jose Garcia de la Torre<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
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