[ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?
Hi, everyone, I want to run plenty secondary structure prediction works and online prediction costs a lot of time. So I expect local software for secondary structure prediction will greatly help to my work. Has anyone ever configed such local secondary structure prediction server? Any suggestion will be welcome. Thanksregards, Yuan SHANG
[ccp4bb] Random coil protein
Dear users, I'm just approaching to a new project...so, I have evidences of an interaction between the N-terminus region of a protein with its own C-terminal domain. The C-terminal domain is perfectly folded (easily expressed and purified), instead of the N-terminal one that is mostly random coil. I would like to express and crystallize the complex between them. I'm wondering if anyone could give me tricks how to express the random coils portion in E. coli and keeping it in a soluble form. Could co-expression help? Thank you in advance, all the best, Marco
Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?
Hi, I would just submit your sequence to Phyre (http://www.sbg.bio.ic.ac.uk/~phyre/). You'll get, among other good things, the secondary structure predictions, perhaps even a 3-D structure prediction, depending on the similarity of your sequence to that of known structures. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 商元 [shangyuan5...@gmail.com] Sent: Sunday, December 04, 2011 2:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server? Hi, everyone, I want to run plenty secondary structure prediction works and online prediction costs a lot of time. So I expect local software for secondary structure prediction will greatly help to my work. Has anyone ever configed such local secondary structure prediction server? Any suggestion will be welcome. Thanksregards, Yuan SHANG
Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?
I highly recommend SABLE if you want to set up your own internal tool. It's pretty easy. http://sable.cchmc.org/ Adamczak, Porollo and Meller, Proteins 56, 2004 SABLE uses a lot of PSI-BLAST runs, so plan your system accordingly. Artem On Sun, Dec 4, 2011 at 6:00 AM, 商元 shangyuan5...@gmail.com wrote: Hi, everyone, I want to run plenty secondary structure prediction works and online prediction costs a lot of time. So I expect local software for secondary structure prediction will greatly help to my work. Has anyone ever configed such local secondary structure prediction server? Any suggestion will be welcome. Thanksregards, Yuan SHANG
Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?
You can run psipred yourself locally by downloading the software available here: http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/ You will also require blast and a local sequence database (usually uniref90). Have a look at the README http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/README This gives you a local command line application to run psipred, not a graphical web interface. Anyway if you really want to run a lot of secondary structure prediction jobs that's really what you want. Hope this helps Jose Jose Duarte Laboratory of Biomolecular Research Paul Scherrer Institute 5232 Villigen PSI Switzerland On 12/04/2011 04:22 PM, Boaz Shaanan wrote: Hi, I would just submit your sequence to Phyre (http://www.sbg.bio.ic.ac.uk/~phyre/). You'll get, among other good things, the secondary structure predictions, perhaps even a 3-D structure prediction, depending on the similarity of your sequence to that of known structures. Cheers, Boaz /Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 / // // / / *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 商元 [shangyuan5...@gmail.com] *Sent:* Sunday, December 04, 2011 2:00 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server? Hi, everyone, I want to run plenty secondary structure prediction works and online prediction costs a lot of time. So I expect local software for secondary structure prediction will greatly help to my work. Has anyone ever configed such local secondary structure prediction server? Any suggestion will be welcome. Thanksregards, Yuan SHANG
Re: [ccp4bb] MR problem
Dear Ping, First thing to ask: Do you know with 100% certainty if your crystals contain a complex? If your crystals are large enough (and you have more than one) you can check this on SDS-PAGE or with mass-spec as long as you are sure to remove all surrounding mother liquid that may contaminate your result. Both proteins should be observed very clearly (80%-20% would be a contamination rather than a co-crystal!). Experience tells us that even with high affinity (nanomolar or better) and preformed complexes, still often only one of the two partners will crystallize. Second: does your second protein contain more than one domain? If so, there may be domain movements that obscure the desnity or even lead to a completely wrong MR solution. Try rigid body refinement with individual domains first. If this does not work, try MR with the individual domains. The MR solution of your second protein may also be wrong for any other reason. Check if you can trust the solution based on the statistics provided in the log file. If the LLG is only marginally better after adding the second protein, it will probably be wrong. Check also if there is no real solution hanging around but rejected by the program because (for example) it has just one clash too many. Remy Loris Vrije Universiteit Brussel and VIB On 04/12/11 05:18, Ping Wang wrote: Dear all, Recently I have a dataset with a protein complex including two proteins. Each structure of the single protein is available. When I use phaser to solve the phase, one protein got good density while the other was not so ideal. In order to get a better phase, I try to cut the flexible region of the bad protein. But the result shows no improvement. Does anyone have some suggestion for me? Thanks! Ping
Re: [ccp4bb] MR problem
Dear Ping, First thing to ask: Do you know with 100% certainty if your crystals contain a complex? If your crystals are large enough (and you have more than one) you can check this on SDS-PAGE or with mass-spec as long as you are sure to remove all surrounding mother liquid that may contaminate your result. Both proteins should be observed very clearly (80%-20% would be a contamination rather than a co-crystal!). Experience tells us that even with high affinity (nanomolar or better) and preformed complexes, still often only one of the two partners will crystallize. Second: does your second protein contain more than one domain? If so, there may be domain movements that obscure the desnity or even lead to a completely wrong MR solution. Try rigid body refinement with individual domains first. If this does not work, try MR with the individual domains. The MR solution of your second protein may also be wrong for any other reason. Check if you can trust the solution based on the statistics provided in the log file. If the LLG is only marginally better after adding the second protein, it will probably be wrong. Check also if there is no real solution hanging around but rejected by the program because (for example) it has just one clash too many. Remy Loris Vrije Universiteit Brussel and VIB On 04/12/11 05:18, Ping Wang wrote: Dear all, Recently I have a dataset with a protein complex including two proteins. Each structure of the single protein is available. When I use phaser to solve the phase, one protein got good density while the other was not so ideal. In order to get a better phase, I try to cut the flexible region of the bad protein. But the result shows no improvement. Does anyone have some suggestion for me? Thanks! Ping
[ccp4bb]
http://science.loriz.ca/lipids/includes/templates/imagec.html
[ccp4bb] Job Opportunity - Head of the Berkeley Center for Structural Biology
The Physical Biosciences Division at Lawrence Berkeley National Laboratory is seeking candidates for the Head of the Berkeley Center for Structural Biology. This position provides scientific, technical and operational oversight of the BCSB at the Advanced Light Source (ALS), a third generation synchrotron facility. The BCSB is a user resource for structural biology experiments and consists of 5 beamlines at 2 sectors of the ALS, with a staff of 16. This Staff Scientist position will provide leadership and direction to develop methodology and instrumentation for collecting and analyzing crystallographic data using synchrotron radiation, and on projects involving the structure determination of biological molecules using X-ray crystallography. This position focuses on the field of crystallography, and involves interactions and collaborations with researchers from multiple scientific disciplines including chemistry, crystallography, biochemistry, biology, physics and computational sciences. For full details please visit the job application link at: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=enjob=73970 Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more about the Lab at http://www.lbl.gov. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] article about Vladimir Vand
I found an article that might interest some of you in a journal that most crystallographers probably do not read: Alena Solcova, Michal Krizek Vladimir Vand (1911-1968): Pioneer of Computational Methods in Crystallography IEEE Annals of the History of Computing, Vol. 33, No. 4 October-December 2011, pp. 38-44. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 =
