From owner-chemistry@ccl.net Mon Aug 13 04:00:00 2012 From: "Gerard Pujadas gerard.pujadas-,-gmail.com" To: CCL Subject: CCL: Is there any webserver for predicting how to improve the side-chain packing interactions in the hydrophobic core of a protein? Message-Id: <-47360-120813035804-7803-vTcxVJlN6W//A84TbFkzeA:_:server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=e89a8ff1c6e417908504c7210d63 Date: Mon, 13 Aug 2012 09:57:54 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas=-=gmail.com] --e89a8ff1c6e417908504c7210d63 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL list members, first of all, sorry for cross-posting. I wonder if there is any webserver for predicting how to improve the side-chain packing interactions in the hydrophobic core of a protein. Ideally, the user should provide to the webserver a 3D protein structure and obtain a list of regions at the protein core where the side-chain packing is suboptimal and where mutations could improve the stability relative to the one of the native protein. I have found the probe softwareis able to do that but I think that it is a little bit difficult to use for undergraduate students and I am looking for something more easy to use. With many thanks in advances for your help Yours sincerely Gerard -- Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 Nutrigenomics Research Group phone +34 977 55 (9565) Biochemistry and Biotechnology Department Office 106, Building N4, Campus Sescelades Universitat Rovira i Virgili Tarragona, Catalonia --e89a8ff1c6e417908504c7210d63 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL list members,

first of all, sorry for cross-posting.
I wonder if there is any webserver for predicting how to improve the side-= chain packing interactions in the hydrophobic core of a protein. Ideally, t= he user should provide to the webserver a 3D protein structure and obtain a= list of regions at the protein core where the side-chain packing is subopt= imal and where mutations could improve the stability relative to the one of= the native protein. I have found the probe software is able to do that but I thin= k that it is a little bit difficult to use for undergraduate students and I= am looking for something more easy to use.

With many thanks in advances for your help

Yours sincerely
Gerard

--
G= erard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22
Nutrigenomics Research Group
phone +34 977 55 (9565)
Biochemistry and Biotechnology Department
Office 106, Building N4, Campu= s Sescelades
Universitat Rovira i Virgili
Tarragona, Catalonia=

--e89a8ff1c6e417908504c7210d63-- From owner-chemistry@ccl.net Mon Aug 13 08:24:01 2012 From: "Alcides Simao alsimao(-)gmail.com" To: CCL Subject: CCL: Is there any webserver for predicting how to improve the side-chain packing interactions in the hydrophobic core of a protein? Message-Id: <-47361-120813050014-14648-PTndPmApLonIYdcypqJStw|-|server.ccl.net> X-Original-From: Alcides Simao Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 13 Aug 2012 11:00:09 +0200 MIME-Version: 1.0 Sent to CCL by: Alcides Simao [alsimao.:.gmail.com] Hello! I am not very familiar with this type of studies, but I believe that you can use VEGA ZZ and/or TINKER to help you out. Both of them can be set up as a webtool. Just my 0.2 cents... All the best, Alcides From owner-chemistry@ccl.net Mon Aug 13 08:59:00 2012 From: "Azin Naghmeh Azarkamand Azin.Azarkamand]~[gmail.com" To: CCL Subject: CCL: structure of amorph silica, simulation Message-Id: <-47362-120813061711-16419-1ohQo01JTmYhSHkHdbE9Zw|a|server.ccl.net> X-Original-From: "Azin Naghmeh Azarkamand" Date: Mon, 13 Aug 2012 06:17:10 -0400 Sent to CCL by: "Azin Naghmeh Azarkamand" [Azin.Azarkamand!=!gmail.com] Dear CCL'ers I am writing in order to find the data for forming the structure of amorph silica. I would like to form this structure but since every work that has been published involved the simulating of the mentioned structure and I have not worked with simulation programs before so I would be grateful If you could supply me with this data. Thanks in advance Faithfully