[ccp4bb] Scientist 1, Structural Biology at Plexxikon Inc. in Berkeley, CA
Dear all, Plexxikon is a leader in the discovery and development of novel, small molecule pharmaceuticals. The company has utilized its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage programs in a number of therapeutic areas. Plexxikon's most advanced program, Zelboraf(tm) (vemurafenib, and formerly known as PLX4032), has recently been approved by the FDA. Plexxikon's demonstrated capability in discovery and early development uniquely positions the company to develop multiple commercial franchises for different therapeutic indications, and create significant value for Plexxikon and its collaborators. Plexxikon's novel discovery approach, combined with an experienced management and scientific team, a broad network of scientific and clinical experts, and partnerships that support later stage development, have been key drivers of the company's success since it began operations in 2001. In April 2011, Plexxikon became a member of the Daiichi Sankyo Group, and continues to build its broad and diverse pipeline. Plexxikon is a small business with less than 50 employees and this position will be a critical member of the Structural Biology team reporting to an experienced scientist. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. For job responsibilities and Position requirements, please see the following website. http://www.jobscore.com/jobs/plexxikon/scientist-1-structural-biology/dRQ0Garwur4QOteJe4efaV?Board=Indeed&PID=937159 If you are interested, please apply through the same link. Best Regards, Ying Zhang Scientist Plexxikon Inc.
[ccp4bb] "Difference" set of contacts
Hi all- I have 2 PDB files of the same protein (in slightly different states) and I want to output a table of interactions (preferably hydrogen bonds, salt bridges) that are unique to a structure i.e. Ser22 OG forms a hydrogen bond to Lys25 NZ in structure 1 but not in structure 2. In other words, I'd like to generate a difference set of contacts. Is there a way I can run NCONT or CONTACT or other software (or nifty scripting) to do this? Thanks and have a nice weekend- Brad
Re: [ccp4bb] Expert opinion for optimizing ethylene glycol crystallization condition
Shankar, I would suggest to also set up a few plates with your protein in HEPES instead of Tris. I once worked for months trying to improve tiny crystals while my protein was in Tris, pH 7.4, to no avail. I got beautiful crystals when I purified my protein in HEPES, pH 7.4, with everything else the same. HTH, Cale On Fri, Jan 4, 2013 at 11:11 AM, Sankaranarayanan Srinivasan < texs...@gmail.com> wrote: > Dear all, > > Thank you very much for all your helpful comments. I will try them and > post on the BB my results. > > Best regards > > Shankar > > > On Wed, Jan 2, 2013 at 11:59 AM, Sankaranarayanan Srinivasan < > texs...@gmail.com> wrote: > >> Dear all, >> >> A very happy new year to all. >> >> I would appreciate some expert advice on optimizing a crystallization >> condition in which the initial hits were obtained with ethylene glycol as >> the main precipitant. Here is the summary of things tried. >> >> We have a protein, size (31Kda) and the starting protein buffer is 0.1M >> Tris pH7.5, 0.1M NaCl, 10% glycerol. >> The initial crystal hit was obtained from the emerald cryo kit condition >> that has 0.1M imidazole pH 8.0 , 50% (v/v) ethylene glycol. The crystals >> were tiny (10-20um). A crystallization matrix to obtain better crystals >> by varying the imidazole pH and ethylene glycol concentrations was tried >> from which the best condition obtained was 0.1M imidazole pH 6.5 , 30% >> (v/v) ethylene glycol. The crystals were slightly bigger 50um. >> On trying the additive screen, bigger crystals (200um) were obtained, but >> putting them under the x-ray beam with direct freezing did not yield any >> diffraction spots. >> Trying other cryo-conditions like glycerol and 50-50 paratone/oil mixture >> also yielded similar results. >> Low resolution spots near the beam stop were also not seen. Similarly >> spots indicative of salt was also not seen. It just had hazy ice rings kind >> of stuff. (The beam was definitely on the crystal) >> To check if what we have was salt, a control condition with no protein >> was tried. Also the crystals were run on a gel after thorough washing. Both >> these tests, show that they are definitely protein crystals and not salt. >> Seeding also did not yield any improved crystals. >> I was suggested using di-ethylene glycol, propane diol as alternatives. >> I would greatly appreciate if you can give your opinion on using other >> di-alcohols as precipitants or other ways to improve these crystals. >> I tried searching the PDB to see if someone had actually used ethylene >> glycol as a precipitant, most of them were used as a cryo condition than >> actually as a precipitant. >> >> Thank you very much in advance. >> >> Regards >> Shankar Srinivasan >> >> >
Re: [ccp4bb] Who invented PDB format?
I love this footnote from the JMB paper: " Requests should be accompanied with a new 2400 ft reel of magnetic tape, and a check or purchase order for U.S. $34.30 made to the order of Brookhaven National Laboratory, to cover postage and handling. This charge is subject to change in the future." -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Santarsiero, Bernard D. Sent: Friday, January 04, 2013 3:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Who invented PDB format? On Fri, January 4, 2013 2:31 pm, Carter, Charlie wrote: > While I cannot be sure about the format, the original PDB was the creation > of Edgar Meyer, Walter Hamilton, and Helen Berman. Hamilton was at > Brookhaven, which held the database until 1994. It passed to the Rutgers > consortium in 1998. It is likely that the format, which hasn't changed > appreciably for at least 30 years, was their creation. Helen, obviously, > is still at the helm, having resumed PDB leadership with the Rutgers > consortium, and she would certainly know who devised the original format. > > Charlie > > On Jan 4, 2013, at 3:17 PM, Frank von Delft wrote: > >> Some spam for your Friday night: does anybody know who invented the PDB >> file format originally? >> >> (We're at the Study Weekend dinner, and Keith Wilson's memory has failed >> us all...) > > -- Bernard D. Santarsiero Associate Director, UICentre Research Professor Center for Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy Center for Structural Biology Center for Clinical and Translational Science University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Who invented PDB format?
Charlie is correct about who established the PDB in 1971 and I assume that it was their decision to use Diamond format initially. When I started at the PDB in summer 1974 there already were 14 entries, in Diamond format. 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 = On Fri, 4 Jan 2013, Carter, Charlie wrote: While I cannot be sure about the format, the original PDB was the creation of Edgar Meyer, Walter Hamilton, and Helen Berman. Hamilton was at Brookhaven, which held the database until 1994. It passed to the Rutgers consortium in 1998. It is likely that the format, which hasn't changed appreciably for at least 30 years, was their creation. Helen, obviously, is still at the helm, having resumed PDB leadership with the Rutgers consortium, and she would certainly know who devised the original format. Charlie On Jan 4, 2013, at 3:17 PM, Frank von Delft wrote: Some spam for your Friday night: does anybody know who invented the PDB file format originally? (We're at the Study Weekend dinner, and Keith Wilson's memory has failed us all...)
Re: [ccp4bb] Who invented PDB format?
While I cannot be sure about the format, the original PDB was the creation of Edgar Meyer, Walter Hamilton, and Helen Berman. Hamilton was at Brookhaven, which held the database until 1994. It passed to the Rutgers consortium in 1998. It is likely that the format, which hasn't changed appreciably for at least 30 years, was their creation. Helen, obviously, is still at the helm, having resumed PDB leadership with the Rutgers consortium, and she would certainly know who devised the original format. Charlie On Jan 4, 2013, at 3:17 PM, Frank von Delft wrote: > Some spam for your Friday night: does anybody know who invented the PDB file > format originally? > > (We're at the Study Weekend dinner, and Keith Wilson's memory has failed us > all...)
Re: [ccp4bb] Who invented PDB format?
Are you referring to the format that resembled "Diamond" format (Bob Diamond, not the synchrotron) that we used at the PDB for the first 100 or so entries. Or are you referring to the format that everyone now refers to as PDB format? I had to reprocess the first 100 entries from the original format into "PDB format". Diamond format was based on the output format of the Diamond real-space refinement format and used 132 columns. PDB format was designed by Tom Koetzle, Graheme Williams, and Larry Andrews with input from others, including me. On page http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/newsletters/newsletter.html#pre1999 you can find the old PDB publications. Newsletter 1 has a description of Diamond format and Newsletter 2 has a description of PDB format in its original version. Any other questions? 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 = On Fri, 4 Jan 2013, Frank von Delft wrote: Some spam for your Friday night: does anybody know who invented the PDB file format originally? (We're at the Study Weekend dinner, and Keith Wilson's memory has failed us all...)
[ccp4bb] Who invented PDB format?
Some spam for your Friday night: does anybody know who invented the PDB file format originally? (We're at the Study Weekend dinner, and Keith Wilson's memory has failed us all...)
Re: [ccp4bb] Expert opinion for optimizing ethylene glycol crystallization condition
Dear all, Thank you very much for all your helpful comments. I will try them and post on the BB my results. Best regards Shankar On Wed, Jan 2, 2013 at 11:59 AM, Sankaranarayanan Srinivasan < texs...@gmail.com> wrote: > Dear all, > > A very happy new year to all. > > I would appreciate some expert advice on optimizing a crystallization > condition in which the initial hits were obtained with ethylene glycol as > the main precipitant. Here is the summary of things tried. > > We have a protein, size (31Kda) and the starting protein buffer is 0.1M > Tris pH7.5, 0.1M NaCl, 10% glycerol. > The initial crystal hit was obtained from the emerald cryo kit condition > that has 0.1M imidazole pH 8.0 , 50% (v/v) ethylene glycol. The crystals > were tiny (10-20um). A crystallization matrix to obtain better crystals > by varying the imidazole pH and ethylene glycol concentrations was tried > from which the best condition obtained was 0.1M imidazole pH 6.5 , 30% > (v/v) ethylene glycol. The crystals were slightly bigger 50um. > On trying the additive screen, bigger crystals (200um) were obtained, but > putting them under the x-ray beam with direct freezing did not yield any > diffraction spots. > Trying other cryo-conditions like glycerol and 50-50 paratone/oil mixture > also yielded similar results. > Low resolution spots near the beam stop were also not seen. Similarly > spots indicative of salt was also not seen. It just had hazy ice rings kind > of stuff. (The beam was definitely on the crystal) > To check if what we have was salt, a control condition with no protein was > tried. Also the crystals were run on a gel after thorough washing. Both > these tests, show that they are definitely protein crystals and not salt. > Seeding also did not yield any improved crystals. > I was suggested using di-ethylene glycol, propane diol as alternatives. > I would greatly appreciate if you can give your opinion on using other > di-alcohols as precipitants or other ways to improve these crystals. > I tried searching the PDB to see if someone had actually used ethylene > glycol as a precipitant, most of them were used as a cryo condition than > actually as a precipitant. > > Thank you very much in advance. > > Regards > Shankar Srinivasan > >
[ccp4bb] Deadline: 4 February -- Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Crystallographer/Structural biologist to support anti-cancer drug discovery in Newcastle
Dear (and hopefully still festive) all, We would like to draw attention to an opportunity to join the structural biology laboratory of Martin Noble and Jane Endicott in the Northern Institute for Cancer Research, Newcastle University. This post, funded for up to 2 years by the MRC/DPFS, is for a crystallographer to join a team of clinical and translational researchers who are developing inhibitors of a promising kinase pathway as a potential novel strategy for the treatment of a range of tumors. The project is at an extremely exciting stage, and the timeline for appointment is therefore rather short: The deadline for applications is 15th January, and shortlisted candidates will be notified by e-mail before Friday January 18th. Interviews will take place on Thursday January 24th. Application is through the Newcastle University website, via the URL: https://www15.i-grasp.com/fe/tpl_newcastle02.asp?newms=jj&id=47164&aid=14216 Best wishes, Martin Noble and Jane Endicott
[ccp4bb] archive of talks from 2013 study weekend
Dear All some people have asked if the talks will be archived. We will make the majority of the talks available as sessions on this site http://87.83.31.218/tcs/#page:recordingList&pageNumber:1 Unfortunately some of the talks contain sensitive material, so we will not be archiving those talks. The sessions will be accessible for about 1 week before we remove them. Charles Ballard CCP4 ps - for none windows users VLC will work as per the last e-mail I sent -- Scanned by iCritical.
[ccp4bb] Postdoctoral Scientist at Oxford University
Dear All - We would have a position available for a Postdoctoral Scientist at the SGC (Oxford University) Nuffield Department of Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford The PDF will work in the epigenetic probe project working on protein ligand complexes and the characterization of protein ligand interactions. A strong background in protein biochemistry is also required - Here is a link to the application https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=106036 and links to our group home pages - http://www.thesgc.org/scientists/groups/oxford/chembio http://www.tdi.ox.ac.uk/chemical-biology Best regards Stefan
Re: [ccp4bb] streaming of the 2013 CCP3 Study Weekend
For the unfamiliar, like myself, the URL for VLC is mms://87.83.31.218/stfc On a Mac: VLC -> File -> Open Network ... (enter URL above) then click Open
