From yellowish from gmail.com Sun Jun 8 02:54:03 2008 From: yellowish from gmail.com (Protenger) Date: Sun Jun 8 11:47:02 2008 Subject: [Protein-analysis] Lattice vs Off-Lattice models Message-ID: <3888df53-b749-49f4-be73-85112ffd757f@x41g2000hsb.googlegroups.com> Hi all I just have a simple question. what is the deffernce(s) of lattice and off-lattice models in protein folding simulations. Thank you From sticher from bioc.unizh.ch Tue Jun 10 04:48:14 2008 From: sticher from bioc.unizh.ch (Patrick Sticher) Date: Tue Jun 10 07:27:21 2008 Subject: [Protein-analysis] Practical Course in 2D Membrane Crystallization and Observation Message-ID: <484E4DDE.4070203@bioc.unizh.ch> Dear colleagues, please be informed that online applications are accepted for the following course: ** 7TH NCCR PRACTICAL COURSE AND EMBN SUMMER SCHOOL IN 2D MEMBRANE PROTEIN CRYSTALLIZATION AND OBSERVATION October 20 - 24, 2008, Basel, Switzerland www.structuralbiology.uzh.ch/membranecourse2008.asp ** Course topics include Membrane protein expression, solubilization and purification, detergent properties and interactions with lipids and proteins, functional analysis of membrane proteins, 2D-crystallization, electron microscopy of 2D crystals, image processing, application of other techniques: AFM, IR-spectroscopy, solid-state NMR ** Speakers Nora Eifler, Andreas Engel, Joachim Heberle, Ralf Kaldenhoff, Daniel L?vy, Xiao-Dan Li, Daniel J. M?ller, Ansgar Philippsen, Herv? R?migy, ** Keynote lecture by Hartmut Oschkinat The course is primarily directed to PhD students and postdocs with some previous experience in the structural biology of membrane proteins or related fields wishing to learn more on 2D crystallization and EM/AFM observation technologies. A limited number of EU fellowships is available for the support of junior scientists attending this course. The course supported by the European Union Marie Curie Conferences and Training Courses Program, as well as by the Swiss NCCR Structural Biology. In agreement with EU guidelines we would like to particularly encourage female scientists to participate and to apply for financial support. ** Interested candidates are encouraged to apply online on www.structuralbiology.uzh.ch/membranecourse2008.asp. Application deadline will be September 12, 2008. We will be able to accept 25 participants to this course. Best regards, Patrick Sticher P.S. Also this fall: 6th International NCCR Symposium on New Trends in Structural Biology, September 8 + 9, 2008 in Z?rich, Switzerland. Registration and information: www.structuralbiology.uzh.ch/symposium2008.asp ____________________________ Dr. Patrick Sticher Moser NCCR Scientific Officer Institute of Biochemistry University of Z?rich Winterthurerstrasse 190 CH - 8057 Z?rich Phone +41 / (0)44 / 635 54 84 Fax +41 / (0)44 / 635 59 08 Mail sticher@bioc.uzh.ch From Barbara.Delmulle from UGent.be Wed Jun 11 02:50:35 2008 From: Barbara.Delmulle from UGent.be (Barbara Delmulle) Date: Wed Jun 11 14:10:35 2008 Subject: [Protein-analysis] Free Mass Spectrometry Tutorial on CD Message-ID: <003701c8cb97$d4e50c20$53bac19d@nemo> Dear Mr Smith, We have here in our lab the course 'Back to Basics' of Micromass. He is very useful and I want to use some parts to write an article. But the first pages with all the bibliografic data are missing. Would it be possible to send me the author, year, ... which is necessary for the reference list? Thank you very much! Kind regards, Lic. Barbara Delmulle Laboratory of Food Analysis Partner in Food2Know Faculty of Farmaceutical Sciences Ghent University Harelbekestraat 72 B - 9000 Ghent Belgium Tel : 09/264.81.16 Fax : 09/264.81.99 E-mail : Barbara.Delmulle@UGent.be From Barbara.Delmulle from UGent.be Thu Jun 12 01:48:05 2008 From: Barbara.Delmulle from UGent.be (Barbara Delmulle) Date: Thu Jun 12 08:43:15 2008 Subject: [Protein-analysis] Free Mass Spectrometry Tutorial on CD Message-ID: <004c01c8cc58$447f2230$53bac19d@nemo> Hello Mr Smith, Thank you for your answer. What I really like to have is the "author, publisher, date, ...). Kind regards, Lic. Barbara Delmulle Laboratory of Food Analysis Partner in Food2Know Faculty of Farmaceutical Sciences Ghent University Harelbekestraat 72 B - 9000 Ghent Belgium Tel : 09/264.81.16 Fax : 09/264.81.99 E-mail : Barbara.Delmulle@UGent.be From semaz81 from hotmail.com Fri Jun 13 08:28:09 2008 From: semaz81 from hotmail.com (samar z) Date: Fri Jun 13 11:03:49 2008 Subject: [Protein-analysis] protein refolding Message-ID: Dear all,I am a PhD student and I want your help about refolding an enzyme after purification.I induced the enzyme by IPTG but it was found to be insoluble so in order to upload it on a nickel column (as it has His-Tag) I use 6M of urea.After purification, I tried to refold it and remove the urea by dialysis it against Tris buffer 50uM but it precipitated directly. I tried to dialysis it against a gradient of urea with Tris buffer and it didn't work.I tried also to refold it by dilution and it precipitated again.can anyone help me to solve this problem.Thank youSemaz _________________________________________________________________ Discover the new Windows Vista http://search.msn.com/results.aspx?q=windows+vista&mkt=en-US&form=QBREFrom dan.bolser from gmail.com Mon Jun 16 05:26:24 2008 From: dan.bolser from gmail.com (Dan Bolser) Date: Mon Jun 16 11:45:31 2008 Subject: [Protein-analysis] Re: pdb-l: About PDB Files and Secondary Structures In-Reply-To: <4f8cb9900804230425q621e90a7wa41467d7263badf8@mail.gmail.com> References: <4f8cb9900804230425q621e90a7wa41467d7263badf8@mail.gmail.com> Message-ID: <2c8757af0806160326q346638e4ue8e3fbc23d9df82b@mail.gmail.com> 2008/4/23 Narges Habibi : > Hi all, > > I'm doing a project on "Protein Contact Map Prediction" and I use some > features for nueral network's input, including Secondary Structure of a > given Amino Acid. There are several ways: > > 1- getting dssp file for each pdb file (from ftp server) > 2- extracting from pdb file (The HELIX and SHEET and TURN section) > 3- getting ss file from www.pdb.org (as I see the given sequences in this > file don't match with the pdb files, why?) > > What do you suggest? What method is more accurate? I have summarised the various replies to this and similar questions from the archive into the PDB FAQ here: http://pdbwiki.org/index.php/PDB_FAQ#Q:_How_do_I_find.2Fpredict.2Fdisplay_secondary_structure.3F Comments and feedback on this summary are appreciated. Dan. > Thanks in advance > > -- > Narges Habibi > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . > -- hello