From mukhin.m from gmail.com Wed Apr 1 12:42:05 2009 From: mukhin.m from gmail.com (mukhin.m@gmail.com) Date: Wed Apr 1 16:32:21 2009 Subject: [Protein-analysis] mapping KEGG ID to CCD Message-ID: <9c21b144-b53b-4cab-a6b8-609a4819eea0@r31g2000prh.googlegroups.com> Hello, Is anyone familiar with a process to map KEGG IDs to CCDs? For example: http://www.genome.jp/dbget-bin/www_bget?cpd:C00389 Some KEGGs have links to the CCD, as you can see below PDB-CCD: QUE (the CCD uses a 3 letter abbreviation). So besides getting lucky in browsing the KEGG db and finding some CCD links, are there any other databases/websites/applications that link the two? Thank you. ps: this is for ~1000 KEGG ids From darek.kedra from gmail.com Wed Apr 1 19:28:46 2009 From: darek.kedra from gmail.com (darked) Date: Wed Apr 1 23:10:27 2009 Subject: [Protein-analysis] Re: mapping KEGG ID to CCD References: <9c21b144-b53b-4cab-a6b8-609a4819eea0@r31g2000prh.googlegroups.com> Message-ID: <624c6e73-280f-4e80-b6d2-b13b9d406956@z19g2000yqe.googlegroups.com> On Apr 1, 7:42?pm, mukhi...@gmail.com wrote: > Hello, > Is anyone familiar with a process to map KEGG IDs to CCDs? For > example:http://www.genome.jp/dbget-bin/www_bget?cpd:C00389 > > Some KEGGs have links to the CCD, as you can see below PDB-CCD: QUE > (the CCD uses a 3 letter abbreviation). So besides getting lucky in > browsing the KEGG db and finding some CCD links, are there any other > databases/websites/applications that link the two? Thank you. > > ps: this is for ~1000 KEGG ids Just two possible starting points, not tested solutions: 1) Check out this KEGG data file: ftp://ftp.genome.jp/pub/kegg/ligand/compound/compound if it contains what you need (CCD ids in separate rows) one can do some scripting and parse the file. 2) SRS system at EBI http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz darked From warren3 from llnl.gov Thu Apr 2 10:28:06 2009 From: warren3 from llnl.gov (warren3@llnl.gov) Date: Thu Apr 2 11:29:53 2009 Subject: [Protein-analysis] Voyager-DE STR Message-ID: I am in possession of an essentially unused ABI Voyager-DE STR. If you are interested in it for parts or refurbishment feel free to contact me. Fred From microsathese from hotmail.com Mon Apr 6 00:49:03 2009 From: microsathese from hotmail.com (Niraikulam Ayyadurai) Date: Mon Apr 6 09:12:56 2009 Subject: [Protein-analysis] Need a Help to Express my Protein In Reducing condition Message-ID: Dear all I suppose to express my protein under reducing condition in E.coli. Some of them used DTT and Ascorbic acid to prevent the oxidation of my compound in the medium (Minimal Medium). IF my compund oxidized it produce quinones and it is toxic to the E.coli. So please suggest me which reducing agent may be good for my work and how can i overcome the quinone compound production. I deeply appriciate your comments my question thank u _________________________________________________________________ How fun is this? IMing with Windows Live Messenger just got better. http://www.microsoft.com/india/windows/windowslive/messenger.aspx From sticher from bioc.uzh.ch Mon Apr 6 10:20:46 2009 From: sticher from bioc.uzh.ch (Patrick Sticher) Date: Mon Apr 6 11:48:01 2009 Subject: [Protein-analysis] 7th International NCCR Symposium on New Trends in Structural Biology Message-ID: <49DA1DCE.5030901@bioc.uzh.ch> Dear colleagues, please be informed that the registration slot for the 7th International NCCR Symposium on New Trends in Structural Biology 7 + 8 September 2009, ETH Z?rich, Lecture Hall HG E7, Z?rich, Switzerland is now open. Online registration is possible directly from the symposium website: www.structuralbiology.uzh.ch/symposium2009 where you will also find further information about this event. Confirmed plenary lecturer to date: Pietro de Camilli, Arthur Horwich, Brian Kobilka, Harry Noller, Anna Marie Pyle, David Wemmer, Masasuke Yoshida Please do not hesitate to contact me anytime if you need further information (sticher@bioc.uzh.ch). With best regards, Patrick Sticher The NCCR Structural Biology is a research initiative of the Swiss Science Foundation. Its research encompasses the fields of recombinant protein technologies, macromolecular structure determination and computational biomolecular sciences with a special focus on membrane proteins and supramolecular assemblies/interactions. 19 research groups from Swiss Universities and Research Institutions participate in this network. www.structuralbiology.uzh.ch/ _________________________________ 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 -- _________________________________ Visit the NCCR on the Internet www.structuralbiology.uzh.ch 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 akkzou from yahoo.fr Sun Apr 12 08:32:48 2009 From: akkzou from yahoo.fr (zoubida akkouche) Date: Sun Apr 12 12:19:27 2009 Subject: [Protein-analysis] (no subject) Message-ID: <6818.46340.qm@web24502.mail.ird.yahoo.com> Hello, I am a student in Biology at the University of Bejaia in Algeria, I'm preparing my thesis magister (protein-protein interactions of egg whites), I seek a protocol chromatography gel filtration with gel Sephadex G75 to separate the proteins of egg white, actually I'll use the three major proteins of egg white (ovalbumin, lysozyme and ovotransferrine) powder, if you can help me. Also I'd like to understand protein-protein interactions within the cell in general, their different sizes and types and methods used to study them. Thank you and good luck ? From engelbert_buxbaum from hotmail.com Mon Apr 13 08:41:18 2009 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Mon Apr 13 10:55:10 2009 Subject: [Protein-analysis] Re: (no subject) References: Message-ID: Am 12.04.2009, 09:32 Uhr, schrieb zoubida akkouche : > Hello, > I am a student in Biology at the University of Bejaia in Algeria, I'm > preparing my thesis magister (protein-protein interactions of egg > whites), I seek a protocol chromatography gel filtration with gel > Sephadex G75 to separate the proteins of egg white, actually I'll use > the three major proteins of egg white (ovalbumin, lysozyme and > ovotransferrine) powder, if you can help me. > Also I'd like to understand protein-protein interactions within the cell > in general, their different sizes and types and methods used to study Since you did not tell us what you are looking for, advice can be only general. For deparation techniques you should download the booklets available from http://www1.gelifesciences.com/aptrix/upp01077.nsf/Content/orderonline handbooks. That should give you a good idea on theory and practice of the procedures involved. You may also want to get a good book on general laboratory methods in biochemistry, e.g. @book{Sco-94, AUTHOR= {R.K. Scopes}, TITLE= {Protein purification, Principles and Practice}, YEAR= {1994}, PUBLISHER= {Springer}, ADDRESS= {New York}, EDITION= {3}, ISBN= {0-387-94072-3}, LANGUAGE= {engl} } And finally some books to introduce you to to the biology of the field: @book{Hol-06, AUTHOR= {K.E. van Holde and W.C. Johnson and P.S. Ho}, TITLE= {Principles of physical biochemistry}, YEAR= {2006}, PUBLISHER= {Pearson}, ADDRESS= {Upper Saddle River, N.J.}, EDITION= {2}, LANGUAGE= {engl}, ISBN= {0-13-046427-9} } @book{Lod-00, AUTHOR= {H. Lodish and others}, TITLE= {Molecular Cell Biology}, YEAR= {2008}, PUBLISHER= {W.H. Freeman and Company}, ADDRESS= {New York}, EDITION= {Sixth}, LANGUAGE= {engl} } @book{Alb-08, AUTHOR= {B. Albers and others}, TITLE= {Molecular Biology of the Cell}, YEAR= {2008}, PUBLISHER= {Garland Science}, ADDRESS= {New York}, EDITION= {Fifth}, LANGUAGE= {engl} ISBN= {0-8153-4105-9}, } From jflood from chem.utoronto.ca Mon Apr 13 14:01:45 2009 From: jflood from chem.utoronto.ca (jflood@chem.utoronto.ca) Date: Mon Apr 13 14:44:17 2009 Subject: [Protein-analysis] Fwd: Phe Auxotrophic E. Coli BL21(DE3) Message-ID: <20090413150145.vs0zoqryecoc0kc0@mail.chem.utoronto.ca> Hello, I'm looking for a Phe auxotrophic strain of E Coli that can be used with plasmids with T7 promoter. Preferably BL21 (DE3). Can anybody direct me to a bank, lab or were to buy it? Thnxs From clement from bio.mls.eng.osaka-u.ac.jp Tue Apr 14 22:21:42 2009 From: clement from bio.mls.eng.osaka-u.ac.jp (Clement Angkawidjaja) Date: Wed Apr 15 12:01:28 2009 Subject: [Protein-analysis] Re: Phe Auxotrophic E. Coli BL21(DE3) In-Reply-To: <200904141705.n3EH56h28649@net.bio.net> References: <200904141705.n3EH56h28649@net.bio.net> Message-ID: <2C22A6F1A435412A8398290E87E734A3@Clement> Hi, The pheA-deleted mutant of E coli K12 (strain JW2580) is available for purchase from the National Bioresource project, Japan (http://www.shigen.nig.ac.jp/ecoli/strain/top/top.jsp). You can order it online. You can introduce lambda-DE3 using the lambda-DE3 lysogenation kit provided by Novagen. Hope this helps. Clement Angkawidjaja, Ph.D Specially Appointed Assistant Professor Laboratory of Molecular Biotechnology Division of Advance Science and Biotechnology Osaka University GSE Common East 8F 2-1 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan Tel/fax: +81-6-6879-4580 ----- Original Message ----- From: To: Sent: Wednesday, April 15, 2009 2:05 AM Subject: Proteins Digest, Vol 47, Issue 4 > Send Proteins mailing list submissions to > proteins@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/proteins > or, via email, send a message with subject or body 'help' to > proteins-request@net.bio.net > > You can reach the person managing the list at > proteins-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Proteins digest..." > > > Today's Topics: > > 1. Fwd: Phe Auxotrophic E. Coli BL21(DE3) (jflood@chem.utoronto.ca) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Apr 2009 15:01:45 -0400 > From: jflood@chem.utoronto.ca > Subject: [Protein-analysis] Fwd: Phe Auxotrophic E. Coli BL21(DE3) > To: cellbiol@magpie.bio.indiana.edu, proteins@magpie.bio.indiana.edu, > methods@magpie.bio.indiana.edu > Message-ID: <20090413150145.vs0zoqryecoc0kc0@mail.chem.utoronto.ca> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > > Hello, I'm looking for a Phe auxotrophic strain of E Coli that can be > used with plasmids with T7 promoter. Preferably BL21 (DE3). Can > anybody direct me to a bank, lab or were to buy it? Thnxs > > > > > ------------------------------ > > _______________________________________________ > Proteins mailing list > Proteins@net.bio.net > http://www.bio.net/biomail/listinfo/proteins > > End of Proteins Digest, Vol 47, Issue 4 > *************************************** From ijgmb from acadjourn.org Tue Apr 28 04:32:33 2009 From: ijgmb from acadjourn.org (International Journal of Genetics and Molecular Biology) Date: Tue Apr 28 13:06:17 2009 Subject: [Protein-analysis] call for papers Message-ID: *International Journal of Genetics and Molecular Biology* *www.academicjournals.org/IJGMB * Introducing =91=91International Journal of Genetics and Molecular Biology= =94 * * Dear Colleague, The *International Journal of Genetics and Molecular Biology (IJGMB)* is a multidisciplinary peer-reviewed journal published that will be monthly by Academic Journals (http://www.academicjournals.org/IJGMB ). IJGMB is dedicated to increasing the depth of Genetics and Molecular Biology across disciplines with the ultimate aim of improving Genetics and Molecular Biology research. *Call for Papers* IJGMB will cover all areas of Genetics and Molecular Biology. The journal welcomes the submission of manuscripts that meet the general criteria of significanc= e and scientific excellence, and will publish: =B7 Original articles in basic and applied research =B7 Case studies =B7 Critical reviews, surveys, opinions, commentaries and essays We invite you to submit your manuscript(s) to ijgmb@acadjourn.org for publication in the Maiden Issue (March 2009). Our objective is to inform authors of the decision on their manuscript(s) within four weeks of submission. Following acceptance, a paper will normally be published in the next issue. Instruction for authors and other details are available on our website; http://www.academicjournals.org/IJGMB/Instruction.htm IJGMB is an Open Access Journal One key request of researchers across the world is unrestricted access to research publications. Open access gives a worldwide audience larger than that of any subscription-based journal ad thus increases the visibility and impact of published work. It also enhances indexing, retrieval power and eliminates the need for permissions to reproduce and distribute content.IJGMB is fully committed to the Open Access Initiative and will provide free access to all articles as soon as they are published. Best regards, *Bazim Adigwerex* Editorial Assistant International Journal of Genetics and Molecular Biology E-mail: ijgmb@acadjourn.org www.academicjournals.org/IJGMB