[ccp4bb] protein interactions
Anybody know of any software out there that can predict potential interaction sites between two proteins? They have been shown to interact via y2h screens but I have no idea if they would interact on their own in vitro. Before I clone them into a vector and purify them I would like some sort of confirmation that the interaction could occur in the absence of other cellular factors. There are 2 interactions I am looking at. For the one, the structures of both proteins are known. For the other only one structure is known. So, is there software that uses 2 known structures to predict binding sites and (I know this is a long shot), but is there any software around that could predict an interaction based on the sequences only (or one 3D structure and one sequence)? Thanks Careina
[ccp4bb] Protein volume
Dear all I have two membrane protein structures. Is there any tool to calculte the volume of transmembrane domain and solublle domain separately for comparison? Thank you.
Re: [ccp4bb] protein interactions
Hi Careina, For the first question, it sounds as though IBIS would do what you want: http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi. It will also try to answer your second question, although sequences are compared to known structures, so if your sequence is dissimilar to anything in the PDB it won't work. It looks as though you can only put in one query sequence/structure and will then have to scan the results for the appearance of the second. I hope this helps. -- David On 6 September 2012 07:43, Careina Edgooms careinaedgo...@yahoo.com wrote: Anybody know of any software out there that can predict potential interaction sites between two proteins? They have been shown to interact via y2h screens but I have no idea if they would interact on their own in vitro. Before I clone them into a vector and purify them I would like some sort of confirmation that the interaction could occur in the absence of other cellular factors. There are 2 interactions I am looking at. For the one, the structures of both proteins are known. For the other only one structure is known. So, is there software that uses 2 known structures to predict binding sites and (I know this is a long shot), but is there any software around that could predict an interaction based on the sequences only (or one 3D structure and one sequence)? Thanks Careina
Re: [ccp4bb] Protein volume
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear, you should split the structure into several PDB-files and use the program 'volume' on each. Tim On 09/06/2012 09:58 AM, Theresa Hsu wrote: Dear all I have two membrane protein structures. Is there any tool to calculte the volume of transmembrane domain and solublle domain separately for comparison? Thank you. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQSG/gUxlJ7aRr7hoRAlt1AKCYKnMM2tFYYBbiwXZPTVO7/dR0UgCgy2rF OhCe6wrsITRrv4r+Oux8ZGk= =Rkoa -END PGP SIGNATURE-
[ccp4bb] DEADLINE TOMORROW: Murnau Conference 2012 on Structural Biology of Molecular Transport
Dear colleagues, the registration deadline for the Murnau Conference 2012 on Structural Biology of Molecular Transport is 7 September- TOMORROW! Please take this last chance to register: http://www.murnauconference.de/2012/registration.html. Murnau Conference 2012 on Structural Biology of Molecular Transport October 17-20, 2012 - Murnau/Germany SESSIONS I Channels and Transporters I: Transport through Membrane II RNA, Nuclear and ER Transport / Nucleocytoplasmic Transport III Endosomal / Synaptic Transport IV Cytoskeleton and Cellular Motility V Channels and Transporters II: Molecular Machines PLENARY SPEAKERS Marc Baldus (Utrecht) Tamir Gonen (Washington) Reinhard Jahn (Göttingen) Hartmut Michel (Frankfurt) You Min Chook (Dallas) Poul Nissen (Arhus) Tom Pollard (New Haven) Jim Rothman (Yale) Mike Rosen (Dallas) Helen Saibil (London) Irmi Sinning (Heidelberg) Daniela Stock (Darlinghurst) Gerhard Wagner (Harvard) BACKGROUND INFO The Murnau Conference is an international meeting covering current issues in the wide field of modern structural biology. A clear goal of the conference, which will take place this year for the 4th time, is to bring together the most eminent scientists in the field with young researchers in a casual atmosphere in the heart of Europe. The first three meetings in the series took place in 2005 (Structural Biology of Molecular Recognition), 2007 (Structural Biology of Disease Mechanisms) and 2010 (Structural Biology of the Modern RNA World). Murnau is a picturesque small town located directly at lake Staffelsee in the Bavarian alpine upland between Munich and Garmisch-Partenkirchen. There will be an exciting social program including a typical Bavarian evening in a fashionable microbrewery and ample time for stimulating discussions with participants from all over the world. Please contact us in case of further questions. With best regards, Prof. Dr. Dirk Heinz in the name of the organization committee www.murnauconference.dehttp://www.murnauconference.de murnauconference2...@gmail.commailto:murnauconference2...@gmail.com Murnau Conference 2012 -Office- Christine Bentz GF/W (Scientific Director's Office) Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig, Germany christine.be...@helmholtz-hzi.demailto:christine.be...@helmholtz-hzi.de +49 (0)531-6181-1003 Protect the environment - please don't print this e-mail unless you really need to Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir'in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
Re: [ccp4bb] scala scaleit problems - GUI bug???
Like Tim says SORTMTZ expects a different format used for unmerged reflection lists. And I think this space in the filename causes the SCALEIT problem - linux operating systems often treat spaces as filename terminators.. But the … marks around a file name are meant to override the space terminator and I don't know why there are no such in the HKLOUT line. Any GUI experts out there??? HKLIN /Users/maryortmayer/Desktop/gere_MAD_nat.mtz HKLOUT /Users/maryortmayer/Desktop/PhD/PmSAMOhemedomainpdb/My solving/gere_MAD_nat_scaleit1.mtz Eleanor On 5 Sep 2012, at 16:11, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Mary, I suppose the error from scaleit comes from working in a directory of which the name contains a space. Create a working directory without spaces and try again. This might be considered a bug in ccp4i: The script adds quotes around the input filename (HKLIN), but not the output filename (HKLOUT). If the latter would happen, this error might not occur. Scala fails because it calls sortmtz, and sortmtz expects columns of the names M/ISYM and BATCH which are indeed not present in rnase25.mtz, i.e. this failure is not a bug. Best regards, Tim On 09/05/2012 04:07 PM, Mary Ortmayer wrote: Hi, Thanks for your email Ed, here are the log files. Mary - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQR2uKUxlJ7aRr7hoRAlG/AKCu942PC1HwjcoBtFmqNFVmccs6AgCgtn0b FpbdRg058mEhx9Vb6057/f4= =/EaO -END PGP SIGNATURE-
Re: [ccp4bb] protein interactions
Hi Careina, In answer to your first question you could also try the iPATCH server: http://portal.stats.ox.ac.uk/userdata/proteins/i-Patch/home.pl This takes two reference structures for proteins that interact, and combined with multiple sequence alignments of their homologs attempts to predict the surface contact residues between them. As far as your second question is concerned, a quick google search using the term protein interaction prediction from sequence gave some useful links, one of which is Struct2Net: http://groups.csail.mit.edu/cb/struct2net/webserver/ This tool attempts to predict protein-protein interactions purely from sequence data. However, it does use a structure-based threading approach, so your sequences will be run against the pdb. If they are unique to anything in the structural databases, it may not be useful. Hope this helps, Mohammad Dr. Mohammad W. Bahar Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford ---BeginMessage--- Hi Careina, For the first question, it sounds as though IBIS would do what you want: http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi. It will also try to answer your second question, although sequences are compared to known structures, so if your sequence is dissimilar to anything in the PDB it won't work. It looks as though you can only put in one query sequence/structure and will then have to scan the results for the appearance of the second. I hope this helps. -- David On 6 September 2012 07:43, Careina Edgooms careinaedgo...@yahoo.com wrote: Anybody know of any software out there that can predict potential interaction sites between two proteins? They have been shown to interact via y2h screens but I have no idea if they would interact on their own in vitro. Before I clone them into a vector and purify them I would like some sort of confirmation that the interaction could occur in the absence of other cellular factors. There are 2 interactions I am looking at. For the one, the structures of both proteins are known. For the other only one structure is known. So, is there software that uses 2 known structures to predict binding sites and (I know this is a long shot), but is there any software around that could predict an interaction based on the sequences only (or one 3D structure and one sequence)? Thanks Careina ---End Message---
Re: [ccp4bb] protein interactions
I know this isn't exactly your question, but it doesn't really take that long to clone, express, and purify things nowadays--a few days, even? Also, won't you be doing this anyway? So why not cut out the middle-man? Or, better still, in your cloning downtime, do the software stuff. JPK On Thu, Sep 6, 2012 at 7:20 AM, moham...@strubi.ox.ac.uk wrote: Hi Careina, In answer to your first question you could also try the iPATCH server: http://portal.stats.ox.ac.uk/userdata/proteins/i-Patch/home.pl This takes two reference structures for proteins that interact, and combined with multiple sequence alignments of their homologs attempts to predict the surface contact residues between them. As far as your second question is concerned, a quick google search using the term protein interaction prediction from sequence gave some useful links, one of which is Struct2Net: http://groups.csail.mit.edu/cb/struct2net/webserver/ This tool attempts to predict protein-protein interactions purely from sequence data. However, it does use a structure-based threading approach, so your sequences will be run against the pdb. If they are unique to anything in the structural databases, it may not be useful. Hope this helps, Mohammad Dr. Mohammad W. Bahar Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Hi Careina, For the first question, it sounds as though IBIS would do what you want: http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi. It will also try to answer your second question, although sequences are compared to known structures, so if your sequence is dissimilar to anything in the PDB it won't work. It looks as though you can only put in one query sequence/structure and will then have to scan the results for the appearance of the second. I hope this helps. -- David On 6 September 2012 07:43, Careina Edgooms careinaedgo...@yahoo.comwrote: Anybody know of any software out there that can predict potential interaction sites between two proteins? They have been shown to interact via y2h screens but I have no idea if they would interact on their own in vitro. Before I clone them into a vector and purify them I would like some sort of confirmation that the interaction could occur in the absence of other cellular factors. There are 2 interactions I am looking at. For the one, the structures of both proteins are known. For the other only one structure is known. So, is there software that uses 2 known structures to predict binding sites and (I know this is a long shot), but is there any software around that could predict an interaction based on the sequences only (or one 3D structure and one sequence)? Thanks Careina -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
[ccp4bb] Fwd: 20 Research positions - Ikerbasque
Ikerbasque, the Basque Foundation for Science (Europe), would like to inform you that we have launched an international call to attract 20 senior researchers to the Basque Country (permanent positions). This call is opened until the 30th of September through our website www.ikerbasque.net If you are interested, you can find summarized information about this call following this link: http://www.ikerbasque.net/images/stories/ikerbasque_rp_2012_call_fiche.pdf We would appreciate your help in disseminating this information, in case you know about any colleague that could be interested and meets the requirements of the call. To unsubscribe from this group, please send us an email to ikerbas...@ikerbasque.net Podr ejercitar su derecho de acceso, rectificacin, cancelacin y oposicin mediante envio de un correo electrnico a la siguiente direccin ikerbas...@ikerbasque.net
[ccp4bb] CCP4 Update
Dear CCP4 Users, Following the release of ccp4 6.3.0, CCP4 core team sets up an update mechanism for moderate modifications of Suite's components between the releases. It is expected that updates will be essential for CCP4 maintenance and will make patch releases less frequent or even redundant, while delivering bug fixes and new features much more efficiently than before. Please take a moment to install CCP4 update functionality as described below. While update mechanism will be integrated in all future CCP4 releases, it needs to be installed manually in CCP4 6.3.0. When installed, the updater checks for new updates automatically, and issues a message when new updates are available. After that, updates can be installed in a few mouse clicks. If, for some reason, you find a particular update undesirable, it can be removed with auto-reverting your CCP4 setup to the pre-update state. Note that the update mechanism cannot be used with CCP4 versions lower than 6.3.0, therefore, please upgrade to the latest CCP4 release if you have not done it so far. For upgrade, proceed to CCP4 download pages at http://www.ccp4.ac.uk/download/ . Detail update installation instructions are given in http://www.ccp4.ac.uk/download/update_manual.html The document may seem to be lengthy, however, installation should not take more than a few minutes: 1) download update client (archived) using an appropriate link in the above manual 2) unpack the archive into the top of CCP4 directory ( C:/CCP4/6.3/ in Windows, ccp4-6.3.0/ in Linux/Mac OSX) 3) run the update client (update.exe/update/Update.app) _from CCP4 directory_ by double-clicking on it in your file browser 4) install 1st update 5) (re-)start ccp4i, and see new Manage Updates button in the bottom-right corner of ccp4i window. If this does not work for you for any reason, please (re-)read update manual for details. If that does not help as well, please write to us. Thank you for using CCP4, Eugene Krissinel. -- Scanned by iCritical.
Re: [ccp4bb] Protein volume
Hi Theresa, You can use our free Discovery Studio Visualizer: http://accelrys.com/products/discovery-studio/visualization-download.php You can select the region of choice (in your case the transmembrane domain) and create a surface around it (Structure - Surface - Add). Then in the Molecular Data Table's Surface Tab (View - Data Table), you can find values for the Surface Area as well as Volume. Let me know if you have any trouble with this. Disclaimer: I work for Accelrys. Cheers, Francisco Sr. Product Manager Accelrys.com -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa Hsu Sent: Thursday, September 06, 2012 12:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Protein volume Dear all I have two membrane protein structures. Is there any tool to calculte the volume of transmembrane domain and solublle domain separately for comparison? Thank you.
[ccp4bb] installation in sw or sw64?
I decided to upgrade my MacBook Pro to OS X 8.0 (previously 10.6), and update my coot and CCP4 programs at the same time (now seems like a bad idea). I use the precompiled library from the Scott Lab, so I followed the directions on his website. I did the following: Installed new X11 (from Xquartz) Installed Command Line Tools (OS X Mountain Lion) for Xcode - August 2012 curl -O http://psbmini.ucsc.edu/~wgscott/downloads/fink_for_10.8_64bit_base_install_aptsources_sw.tgz sudo mv fink_for_10.8_64bit_base_install_aptsources_sw.tgz /. sudo tar xvfz fink_for_10.8_64bit_base_install_aptsources_sw.tgz source /sw/bin/init.sh fink selfupdate fink scanpackages sudo apt-get update sudo apt-get dist-upgrade sudo apt-get install coot ccp4 But now Fink is in the /sw directory instead of the /sw64 directory, and the programs like coot seem to only be in the /sw64/bin directory. If I try to run coot after sourcing /sw/bin/init.sh it cannot find coot (because it isn't there), and if I source /sw64/bin/init.sh it runs the older version of coot. What am I do wrong? Should the programs be in /sw or /sw64? Should I delete old /sw64 directory? BTW I got an error message during the installation that Err http://psbmini.ucsc.edu stable/main gcc46-shlibs 4.6.3-1000 404 Not Found Sorry for the dumb question. Bill
Re: [ccp4bb] installation in sw or sw64?
Hi Bill, First of all I would try to completely uninstall (via fink) both ccp4 and coot. In fact the problem is not the location of the programs per se, but the conflict between different versions of the same program. Fink can update the softwares, but not when you rebuild the whole system. Anyway, the latest release of ccp4 suite (6.3.0) doesn't require fink and you can install the entire package (coot included) by downloading the .dmg file from ccp4 website. Moreover, if remember correctly, ccp4 6.3.0 doesn't need X11, too. So, you will be safe proceeding this way. Marco Il giorno giovedì 6 settembre 2012, William N. Zagotta zago...@uw.edu ha scritto: I decided to upgrade my MacBook Pro to OS X 8.0 (previously 10.6), and update my coot and CCP4 programs at the same time (now seems like a bad idea). I use the precompiled library from the Scott Lab, so I followed the directions on his website. I did the following: Installed new X11 (from Xquartz) Installed Command Line Tools (OS X Mountain Lion) for Xcode - August 2012 curl -O http://psbmini.ucsc.edu/~wgscott/downloads/fink_for_10.8_64bit_base_install_aptsources_sw.tgz sudo mv fink_for_10.8_64bit_base_install_aptsources_sw.tgz /. sudo tar xvfz fink_for_10.8_64bit_base_install_aptsources_sw.tgz source /sw/bin/init.sh fink selfupdate fink scanpackages sudo apt-get update sudo apt-get dist-upgrade sudo apt-get install coot ccp4 But now Fink is in the /sw directory instead of the /sw64 directory, and the programs like coot seem to only be in the /sw64/bin directory. If I try to run coot after sourcing /sw/bin/init.sh it cannot find coot (because it isn't there), and if I source /sw64/bin/init.sh it runs the older version of coot. What am I do wrong? Should the programs be in /sw or /sw64? Should I delete old /sw64 directory? BTW I got an error message during the installation that Err http://psbmini.ucsc.edu stable/main gcc46-shlibs 4.6.3-1000 404 Not Found Sorry for the dumb question. Bill
Re: [ccp4bb] poorly diffracting and twinned trigonal crystal
I have a ~4.3 angstrom data set of a trigonal crystal of a seven subunit protein complex which I can scale in P3, P31, P32, P321, P3121 and P3221 with similar statistics: P3 Shell Lower Upper Average Average Norm. Linear Square limitAngstrom I error stat. Chi**2 R-fac R-fac 50.00 9.25 1296.889.223.5 1.233 0.064 0.077 9.25 7.35 356.318.5 9.7 1.512 0.065 0.066 7.35 6.4297.1 8.2 7.5 1.584 0.143 0.140 6.42 5.8355.2 8.3 8.1 1.503 0.247 0.241 5.83 5.4251.4 9.4 9.3 1.438 0.297 0.284 5.42 5.1047.010.510.5 1.469 0.374 0.345 5.10 4.8448.311.811.9 1.421 0.398 0.383 4.84 4.6343.612.913.1 1.474 0.488 0.449 4.63 4.4540.314.114.2 1.530 0.546 0.477 4.45 4.3030.814.715.0 1.601 0.732 0.631 All reflections203.819.612.3 1.477 0.125 0.085 P3121: Shell Lower Upper Average Average Norm. Linear Square limitAngstrom I error stat. Chi**2 R-fac R-fac 50.00 9.14 1242.951.818.3 1.200 0.057 0.068 9.14 7.26 314.011.2 6.5 1.454 0.070 0.069 7.26 6.3586.9 5.3 5.0 1.499 0.158 0.152 6.35 5.7751.9 5.5 5.3 1.248 0.264 0.252 5.77 5.3546.9 6.1 6.0 1.213 0.330 0.305 5.35 5.0444.3 6.9 6.7 1.137 0.393 0.363 5.04 4.7943.4 7.7 7.4 1.109 0.434 0.407 4.79 4.5839.2 8.5 8.1 1.128 0.533 0.478 4.58 4.4034.2 9.1 8.6 1.115 0.634 0.549 4.40 4.2524.9 9.9 9.3 1.064 0.872 0.766 All reflections199.012.4 8.1 1.216 0.127 0.080 Unit cell parameters: 129.653 129.653 358.28090.00090.000 120.000 The systematic absences are consistent with either P31, P32, P3121, or P3221. Analyzing the cell contents in P3121 suggests either 1 (Matthews coefficient of 3.86, 68.2% solvent) or 2 mol/ASU (Matthews coefficient of 1.93, 36.38% solvent) I built a molecular replacement model (a polyala model containing about 2/3 of the protein complex) and ran phaser in multiple space groups with one (for P3121 or P3221) or two (P31, P32) copies of the model. Runs in P32 or P3221 gave no solutions or solutions with TFZ around 4-5. When run in P31 or P3121, phaser output solutions with TFZ 11.0 and what appeared to be good packing. Rigid body refinement on the P3121 solution failed to improve the Rfactor (it hovered around 55.3%). Adding the missing subunits (as polyala chains) based on the phaser solution and refining with rigid body refinement resulted in a model with an Rfree to 48.5. Refining with torsion angle dynamics and restrained group B-factor refinement made the Rfree worse – it jumped up to about 55.6%. The Rwork values were similar to the Rfree values for each attempt. I also tried DEN refinement with similar results. Rigid body refinement of the P31 phaser solution gave an Rfree of about 54.4%. Adding the missing subunits and running rigid body refinement again improved the Rfree to 53.0. Refining with torsion angle dynamics and restrained group B-factor refinement again made the Rfree worse (increased to 54.5%). I analyzed the reflection file processed in P31 using detect_twinning.inp in cns. The data did not appear to be perfectly merohedrally twinned, but in the test for partial merohedral twinning, the twin fraction calculated for “2 along a,b” was 0.475. I repeated rigid body refinement, then torsion angle dynamics with restrained group b-factor using the calculated twinning parameters. This brought the free R down to 46.3%, but caused significant divergence between Rwork and Rfree (Rwork =21.4%(!)). The Rfree is fairly constant across resolution shells, but Rwork drops dramatically with low resolution reflections (In the 50 – 9.14 ang shell, Rwork = 12.3%!). I’m guessing that because the twinning fraction is near 0.5, detwinning is not working. Does anyone have any suggestions about how to successfully refine this structure (assuming it is possible)? Should we average the twin related reflections to generate perfectly twinned data, and if so, how do we do that? Is the twinning likely responsible for our difficulty refining the structure or could there be a problem with the space group assignment? Why does including the partial twinning in our refinement cause Rfree and Rwork to diverge so dramatically? Given the trouble I’ve had so far and the poor quality of the data, I’m about ready to give up on this structure, but if anyone has any ideas please let me know.
