From yogendra from ccmb.res.in Thu Dec 4 05:58:56 2008 From: yogendra from ccmb.res.in (Dr. Yogendra Sharma) Date: Thu Dec 4 12:30:23 2008 Subject: [Protein-analysis] scissile bond Message-ID: <419B6E4639E14B429C7D1AC014B8EE3F@W206B> Hi all Would any body help in letting us to know: how to identify scissile bonds in a protein sequence. Any web based tool or any triplet sequence related with Arg? Thanks Yogendra Sharma From mrnance from lsi.umich.edu Thu Dec 4 15:36:02 2008 From: mrnance from lsi.umich.edu (Mark Nance) Date: Thu Dec 4 17:15:47 2008 Subject: [Protein-analysis] scissile bond Message-ID: <4937F8E3020000B500010431@lsigroupwise01.lsi.umich.edu> Yogendra, You can try Expasy's PeptideCutter: http://www.expasy.ch/tools/peptidecutter/ The fold of the protein is important, because not all cleavage sites are accessible to proteases. Conformation is important, too. There are several protease protection assays where binding of protein / activation / etc. can be monitored by increases or decreases in susceptibility to specific proteases. Mark >>> "Dr. Yogendra Sharma" 12/04/08 5:58 AM >>> Hi all Would any body help in letting us to know: how to identify scissile bonds in a protein sequence. Any web based tool or any triplet sequence related with Arg? Thanks Yogendra Sharma _______________________________________________ Proteins mailing list Proteins@net.bio.net http://www.bio.net/biomail/listinfo/proteins !DSPAM:63,4938156328201137399876! From xlli from i2r.a-star.edu.sg Tue Dec 16 21:14:59 2008 From: xlli from i2r.a-star.edu.sg (Li Xiaoli) Date: Wed Dec 17 00:03:38 2008 Subject: [Protein-analysis] Call for papers for "Data Mining in Protein Interaction Networks" Message-ID: <162B8AFBFBBB2148A9A1B8F9C5753428060B6330@mailbe01.teak.local.net> Dear Colleagues, We are organizing a special session on "Data Mining in Protein Interaction Networks" in ISIBM conference (2009 ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing). Please refer the call for paper in http://www.isibm.org/IJCBS/sessions.html for more information of this special sessions (The main conference web site is at http://www.isibm.org/IJCBS/index.html ). The conference will be held in Shanghai, China in Aug 3-6 and the deadline to submit your paper is February 15, 2009. Please submit your paper to organizer by email Dr. Xiaoli Li, xlli@ntu.edu.sg Dr. Erliang Zeng, zeng@cs.miami.edu -------------------------------------------------------- Call for papers -------------------------------------------------------- Data Mining in Protein Interaction Networks Session Chairs: Dr. Xiaoli Li, School of Computer Engineering, Nanyang Technological University, Singapore, xlli@ntu.edu.sg Dr. Erliang Zeng, Department of Computer Science, University of Miami, USA, zeng@cs.miami.edu Biological processes in the cell are mostly carried out by complex protein interactions between protein molecules. In recent years, high-throughput methods (e.g. yeast-two-hybrid and tandem affinity purification - mass spectrometry etc) for detecting protein-protein interactions (PPIs) have enabled researchers to construct large-scale PPI networks for various species. In these PPI networks, a node represents individual protein, and a link between two corresponding nodes denotes a physical interaction between the protein pair. Such networks provide researchers unprecedented opportunities to develop new bioinformatics methods to discover the novel biological knowledge. The objective of this special session is to disseminate the best research results from cross-disciplinary researchers (biologists, computer scientists and mathematicians etc) working on analysing and mining protein interaction networks. We hope this special session can promote the researchers to exchange ideas, discuss the biological fundamentals, as well as inspire new computational solutions for these interesting and challenging problems. The scope of this special session includes, but not limited to, protein interaction prediction, protein interaction network cleansing, protein complex/functional module detection, network motif discovery, protein function prediction, protein interaction networks and diseases, comparative genomics, PPI network analysis by integrating with other biological resources, network alignment /querying and visualization tools etc. The authors should prepare their manuscripts according to the instructions given in the conference website. Please submit your manuscripts to the session chairs directly (via email) before February 15, 2009. ********************** ANNOUNCEMENT ******************************** We have moved to Fusionopolis! Our official address is: Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis, South Tower, Singapore 138632. Main line: +65 64082000. Main fax: +65 67761378 Please visit http://www.fusionopolis.a-star.edu.sg/ for more information on Fusionopolis. ****************************************************************** Institute For Infocomm Research - Disclaimer This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you." From vasu.nanobiotech91 from gmail.com Wed Dec 17 22:22:58 2008 From: vasu.nanobiotech91 from gmail.com (shrinivas Dengeti) Date: Thu Dec 18 00:09:26 2008 Subject: [Protein-analysis] Anone there to solve my problem Message-ID: hi ...this is shrinivas doin PhD from India i want estimation of lignin from Sugarcane bagasse..protocol .. or else send me the TAPPI standard protocol.. which could help me estmate lignin conc. present in the sugarcane bagasse.. with regards D.shrinivas From vasu.nanobiotech91 from gmail.com Fri Dec 19 01:35:02 2008 From: vasu.nanobiotech91 from gmail.com (shrinivas Dengeti) Date: Fri Dec 19 10:35:26 2008 Subject: [Protein-analysis] help for designing of primer pair Message-ID: hi all... i got sequenced one of my enzyme gene ( xylanse) ..whcih contain all the regulatory elements also But for cloning and expression studies...i want to get the protein coding part only na? so could you help me out in designing the primers containing the sites for R.E's also...whcih are also prsent in the vectors ... for ex:- pEt series vector... Nco I and xho I are required for inserting into the vector.. bye take care With Regarsds D.shrinivas From biospace from noster-it.com Sat Dec 27 01:07:20 2008 From: biospace from noster-it.com (biospace) Date: Sat Dec 27 15:00:57 2008 Subject: [Protein-analysis] Novel Target For Therapeutics Against Staph Infection Message-ID: <3b698655-afaa-4641-b933-b37824fa2f6a@m16g2000vbp.googlegroups.com> Researchers at the Texas A&M Health Science Center Institute of Biosciences and Technology, and the University of Edinburgh have uncovered how a bacterial pathogen interacts with the blood coagulation protein fibrinogen to cause methicillin-resistant Staphylococcus aureus (MRSA) infections, a finding that could aid in developing therapeutics against the potentially deadly disease. nce occurring more commonly in healthcare facilities, but now affecting segments of the general population, MRSA is a bacterial pathogen responsible for a range of diseases from mild skin infection to life-threatening sepsis. Even with antibiotics, these infections can still be fatal. Senior author Magnus H??k, Ph.D. and his colleagues carried out biochemical and structural studies to determine the binding mechanism of clumping factor A (ClfA), a surface protein that plays an important role in the pathogenesis of S. aureus. The group found that ClfA binds to the blood-clotting protein fibrinogen (Fg) at a site that is also responsible for inducing platelet activation and thrombosis (clot inside a blood vessel). Tonny -------------- More bio-med news & videos Portal to share biological information-data between people http://biospace.ethz.ch From Heather.Vincent from manchester.ac.uk Mon Dec 29 12:40:43 2008 From: Heather.Vincent from manchester.ac.uk (Heather Vincent) Date: Mon Dec 29 13:20:15 2008 Subject: [Protein-analysis] The Science of Proteomics, March 2009 Message-ID: <49590B9B.5040703@manchester.ac.uk> The Science of Proteomics, offered by the University of Leeds, is one of a number of online courses run jointly with The University of Manchester. Our distance courses are delivered in a Virtual Learning Environment, which allows us to extend the classroom into the web. Each course, which is paced to suit those in full-time employment, runs over 16 teaching weeks. This course is divided into 10 section as follows:- 1. Protein structure and post-translational modifications 2. An introduction to proteomics 3. An exploration of the choice of material, the handling and storage of samples and the statistical analysis of samples 4. Sample preparation and fractionation techniques 5. A look at HPLC and MudPIT 6. A detailed look at 2-DE 7. An introduction to mass spectrometry looking at the different methods available and how these benefit proteomics 8. Bioinformatics and data analysis 9. Data storage, interchange and retrieval 10. Introduction to Protein Interactions You will find information on all our courses, including fees and a link to the online application form, here : http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any questions, or need advice on the module options, please contact Heather.Vincent@manchester.ac.uk