[ccp4bb] Job posting: Scientist (crystallography) at Frederick National Laboratory for Cancer Research
Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology (crystallography). The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-protein and protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=2127 Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research 8560 Progress Drive, C1012, Frederick, MD 21701 dhirendra.siman...@fnlcr.nih.gov To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Job posting: Scientist-I (Structural biology) at Frederick National Laboratory for Cancer Research
Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology (crystallography). The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-protein and protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=1845 Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research 8560 Progress Drive, C1012, Frederick, MD 21701 dhirendra.siman...@fnlcr.nih.gov To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Job posting: Scientist-I (Structural Biology) position at Frederick National Laboratory for Cancer Research
Hello everyone, The NCI RAS Initiative at Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in biophysics and structural biology. The candidate will join my group and be responsible for the structural characterization of protein-protein and protein-small molecule complexes by crystallography. The candidate will also be a member of the drug discovery team, working closely with computational and medicinal chemists on structure-based drug design approaches for small molecule agent optimization. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/JobDetails.aspx?site=4&id=1460&source=careerarc Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Group Leader - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. *Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701 *USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702 dhirendra.siman...@fnlcr.nih.gov To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Scientist-I (Structural Biology) position at Frederick National Laboratory for Cancer Research
Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist-I with experience in protein chemistry and structural biology. The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=1404 Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. *Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701 *USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702 dhirendra.siman...@fnlcr.nih.gov To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Job opening: Scientist-I (Structural Biology) at Frederick National Laboratory for Cancer Research
Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology. The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=765 Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. *Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701 *USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702 dhirendra.siman...@fnlcr.nih.gov To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Scientist - CryoEM position at Frederick National Laboratory for Cancer Research
Hello everyone, The Frederick National Laboratory for Cancer Research (operated by Leidos Biomedical Research for NCI) is looking for a Scientist with experience in single-particle cryo-electron microscopy to work on multiple large protein-protein complexes in RAS biology. The Frederick National Laboratory hosts National Cryo-EM facility which allows relatively easy access to high-end cryo-electron microscopes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=465 Best wishes, Dhirendra Simanshu To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] NMR Spectroscopy (Sr. Scientist) position at Frederick National Laboratory, MD
Hello everyone, The Frederick National Laboratory for Cancer Research (FNLCR) is looking for an NMR Spectroscopy (Sr. Scientist) an experienced, hands-on NMR Spectroscopist to provide support for multiple projects in a fast-paced environment of a highly collaborative team of biophysicists, chemists, biochemists, structural, cell, and molecular biologists. FNLCR serves as the hub for the NCI RAS Initiative program. One of the major objectives of the RAS Initiative is to carry out structure-based drug discovery to identify lead compounds against RAS-driven cancers. The candidate will join the RAS Initiative and lead the projects on developing and optimizing small molecules for use as RAS inhibitors. Detailed information is attached below. To apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/JobDetails.aspx?site=4&id=276 Best wishes, Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research 8560 Progress Drive, C1012, Frederick, MD 21701 USA ** *NMR Spectroscopy - Sr. Scientist* Job ID: req276 Facility: Frederick: ATRF Location: 8560 Progress Dr, Frederick, MD 21701 USA The Frederick National Laboratory is dedicated to improving human health through discovery and innovation in the biomedical sciences, focusing on cancer, AIDS, and emerging infectious diseases. The RAS Initiative is seeking an experienced, hands-on NMR Spectroscopist to provide support for multiple projects in a fast-paced environment of a highly collaborative team of biophysicists, chemists, biochemists, structural, cell, and molecular biologists. Our focus is to understand the biology of RAS protein/ RAS at the plasma membrane, and to develop therapies for RAS-driven cancers. *KEY ROLES/RESPONSIBILITIES* - Designing, developing, and implementing NMR-based experiments to support drug discovery projects, and characterizing RAS:effector interactions, and RAS:small-molecule interactions in solution, and at the plasma membrane/membrane mimetics. - Developing advanced NMR methods applied to structure-function studies of bio macromolecules, with the goal of understanding their interactions and responses to various ligands, both small molecule compounds and protein binding partners. - Work in a fast-paced environment, providing NMR support to the FNL/NCI RAS Initiative - Work closely with a highly collaborative multidisciplinary team of chemists, biochemists, structural and cell biologists, to discover, develop, and optimize pharmaceutical agents for use as RAS inhibitors - Design and conduct NMR experiments, collect and analyze data - Maintain in-house NMR spectrometer - Solve NMR structures of RAS protein in complexes with relevant small molecule inhibitors - Provide biophysics support for drug/protein interaction analysis - Work independently, however within highly collaborative team environment *BASIC QUALIFICATIONS* - Possession of a doctorate degree from an accredited college or university according to the Council for Higher Education Accreditation. (Additional qualifying experience may be substituted for the required education). Foreign degrees must be evaluated for U.S. equivalency - In addition to the educational requirements, a minimum of five (5) years of post-doctoral experience in protein NMR is required - Working knowledge of multidimensional heteronuclear NMR experiments for elucidation of protein structure - Strong background in NMR spectroscopy - Expertise in protein NMR, including analysis of protein-drug interactions, protein complexes, and proteins on membrane/membrane mimetics - Must be highly collaborative, with excellent communication skills, self-motivated, and team-oriented - Must be able to obtain and maintain a security clearance *PREFERRED QUALIFICATIONS* - Experience with RAS family proteins NMR - Experience with NMR analysis of RAS family proteins interacting with effectors/binding partners - Experience with SPR, ITC, and other biophysical techniques to measure protein-drug interaction is a plus Equal Opportunity Employer (EOE) | Minority/Female/Disabled/Veteran (M/F/D/V) | Drug Free Workplace (DFW) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Team Lead/Senior Scientist (Computational Chemistry) position at Frederick National Laboratory for Cancer Research
(Apologies for the reposting, the web-link now work correctly) Hello everyone, The Frederick National Laboratory for Cancer Research (FNLCR, operated by Leidos Biomedical Research for NCI) is looking for a Team Lead/Senior Scientist (Computational Chemistry). FNLCR serves as the hub for the NCI RAS Initiative program. One of the major objectives of the RAS Initiative is to carry out structure-based drug discovery to identify lead compounds against RAS-driven cancers. The candidate will join the RAS Initiative and lead the projects on developing and optimizing small molecules for use as RAS inhibitors. For detailed information and to apply for this position, please use this link: https://jobs.leidos.com/ShowJob/Id/1530255/Team-Lead-Senior-Scientist-Computational-Chemistry-(NCI)/ Best wishes, Dhirendra Simanshu
[ccp4bb] Team Lead/Senior Scientist (Computational Chemistry) position at Frederick National Laboratory for Cancer Research
Hello everyone, The Frederick National Laboratory for Cancer Research (FNLCR, operated by Leidos Biomedical Research for NCI) is looking for a Team Lead/Senior Scientist (Computational Chemistry). FNLCR serves as the hub for the NCI RAS Initiative program. One of the major objectives of the RAS Initiative is to carry out structure-based drug discovery to identify lead compounds against RAS-driven cancers. The candidate will join the RAS Initiative and lead the projects on developing and optimizing small molecules for use as RAS inhibitors. For detailed information and to apply for this position, please use this link: https://jobs.leidos.com/ShowJob/Id/1499956/Team-Lead-Senior-Scientist-Computational-Chemistry-(NCI)/ Best wishes, Dhirendra Simanshu
[ccp4bb] Scientist - Structural Biology at Frederick National Laboratory (NCI)
Hello everyone, The Frederick National Laboratory for Cancer Research (operated by Leidos Biomedical Research for NCI) is looking for a Scientist (structural biology). Applicant should have a PhD (preferably with postdoctoral experience) in structural biology, computational chemistry, biochemistry, biophysics, or related field. The ideal applicant is expected to have a demonstrable track record of solving multiple protein-ligand structures and experience of working with computational chemists in drug discovery projects. This position is suitable for a rigorous and detail-oriented experimentalist with a desire to continue in a laboratory-focused role. For detailed information and to apply for this position, please use this link: http://jobs.leidos.com/ShowJob/Id/1431203/Scientist-(NCI)/
[ccp4bb] Postdoctoral position in Structural Biology
A post-doctoral position ( S tructural B iology) is available in the RAS initiative at Frederick National Laboratory for Cancer Research (operated by Leidos Biomedical Research for NCI) . Please visit the link below for more details and instructions on how to apply: http://jobs.leidos.com/ShowJob/Id/861827/Post-Doctoral-Fellow-629153-(NCI)/ *JOB DESCRIPTION* The structural biology group in the RAS initiative focuses on structural analysis of KRAS mutants and biologically relevant KRAS activator/effector complexes in support of drug discovery efforts and to further understand the biochemistry of RAS proteins. We are looking for a highly motivated post -doctoral fellow to join our group. Highly motivated candidates who recently obtained a Ph.D. with a strong background in biochemistry, biophysics and structural biology are encouraged to apply. This post-doc will work closely with the protein production group and carry out structural studies on oncogenic KRAS complexed with effectors, GAPs, regulators and small molecules. We use X-ray crystallography, NMR, molecular modeling, and other biophysical techniques for structural characterization. The candidate will be expected to be able to participate in experimental design and to independently conduct experiments in a priority-driven environment. The candidate should have the ability to act both independently and as a part of the RAS team in pursuit of specific research goals and objectives. The structural biology group in the RAS initiative works very closely with the biochemistry and biophysics group, and is well equipped with crystallization robotics, in-house X-ray generator, and has regular access to the synchrotron beamline at Argonne. *Qualifications:* BASIC QUALIFICATIONS - Possession of a doctoral degree from an accredited college/university according to the Council for Higher Education Accreditation (CHEA) in a field related to structural biology, biochemistry, biophysics or computational biology - Foreign degrees must be evaluated for U.S. equivalency - Demonstrated proficiency in protein biochemical and biophysical characterization - Ability to act both independently and as a part of the RAS team in pursuit of specific research goals and objectives - Ability to conduct experiments and evaluate results independently - Experience in crystallization and structure determination of protein-ligand and protein-protein complexes PREFERRED QUALIFICATIONS - Experience working with small GTPases or RAS-related effector proteins and Knowledge of molecular dynamics simulations and protein-ligand docking.
[ccp4bb] Scientist-I (Structural Biology) - Frederick National Lab for Cancer Research
Dear colleagues, We have an opening for a Scientist-I (Structural Biology) position here in Frederick, MD. If not interested, please forward this email to those who might be. To apply for this position and for further details, including a job description and qualifications, please click on the link below: http://jobs.leidos.com/ShowJob/Id/475028/Scientist-I-615658-%28NCI%29/ Thank you Dhirendra *--* *JOB DESCRIPTION * The Scientist I will work in support of the FNL/NCI RAS Initiative. One of the major objectives of the RAS initiative at the Frederick National Lab for Cancer Research (FNLCR) is to conduct structural analysis of KRAS mutants and biologically relevant KRAS activator/effector complexes in support of drug discovery efforts. The Scientist I will be responsible for: 1) carrying out structural studies on KRAS-effector complexes through the entire protein crystallographic process, including construct design, protein purification, biochemical and biophysical characterization, crystallization, X-ray data collection, structure determination and analysis, 2) working closely with an integrated team of protein scientists in the Protein Expression Laboratory (PEL) at the FNLCR, 3) participating in experimental design and to independently conduct experiments in a priority-driven environment, 4) completing projects independently and as part of a team, and providing timely updates of the project progress to their supervisor both informally and by formal report writing, and 5) generating high-quality peer-reviewed publications. Work may involve the use of potentially hazardous chemical, biological, or radiological materials or may be located in areas where such materials are used. May require the use of personal protective equipment and adherence to strict safety protocols. *Qualifications:* *BASIC QUALIFICATIONS* - PhD in structural biology, protein biochemistry, crystallography, or in a related discipline from an accredited college or university appropriate to biomedical research, or eight (8) years’ experience in lieu of degree - Foreign degrees must be evaluated for U.S. Equivalency - In addition to the educational requirements the candidate will need proven ability in all aspects of protein crystallography from construct design through structure determination and interpretation - Extensive experience in crystallization of protein-ligand and protein-protein complexes - Experience collecting data at synchrotron beamline and solving ab initio structures - Expertise in commonly used crystallography software packages - Proficiency in protein biochemical and biophysical characterization - Record of publications in peer-reviewed journals *PREFERRED QUALIFICATIONS* - Relevant postdoctoral experience in a structural biology laboratory. - Experience working with small GTPases, RAS-related activator/effector proteins, or membrane-associated complexes. - Knowledge of molecular dynamics simulations and protein-ligand docking. *To apply*, click here: http://jobs.leidos.com/ShowJob/Id/475028/Scientist-I-615658-%28NCI%29/
Re: [ccp4bb] Cadmium sites and co-ordinations in structure
Hello Sandeep, I have been in this situation many times before but with different metal ions.. I have found papers published by Marjorie M Harding very useful in such situations. In fact, there are lots of information on-line on which is available here (including all the references for his papers): *METAL COORDINATION SITES IN PROTEINS* * * http://tanna.bch.ed.ac.uk/ http://tanna.bch.ed.ac.uk/qg3.htm http://tanna.bch.ed.ac.uk/newtargs_06.html You will at least find information for Ca and Co here for sure. All the best Simanshu On Fri, Aug 26, 2011 at 10:21 AM, Partha Chakrabarti wrote: > Hi Sandeep, if someone sends one, kindly share the references. > > In general, Ca2+ could have more Asp, Asn kind of coordination and > distorted pentagonal bipyramidal geometry with waters (about 2.5A), Cd can > also have S- since it is softer, I guess Co might have N/O/S (i.e all three > with paired electrons). An inorganic chemistry textbook like Greenwood & > Earnshaw or Cotton & Wilkinson could be handy.. or a bioinorganic chemistry > book. > > HTH, > Partha > > > > > On Fri, Aug 26, 2011 at 7:24 PM, Sandeep wrote: > >> Hi, >> >> I crystallised a protein in the presence of Calcium, Cobalt, and Cadmium >> and determined its structure. It turns out that I see several metal sites in >> the structure, mostly cadmiums. Is there any information published >> (preferably a review) which summarises data on cadmium sites in proteins >> such as for example the possible coordination numbers of cadmium, distances, >> type of side chains found to coordinate with cadmium, etc.? I could extract >> all this from the PDB, but a nice review would be simpler to start with. >> >> Thank you in advance for your help >> >> Sandeep >> > > -- Dhirendra K Simanshu Memorial Sloan-Kettering Cancer Center Structural Biology Program New York, NY, USA 10065
Re: [ccp4bb] phosphate v sulfate
Hello, Thanks for this interesting poll! I have had similar doubt couple of times in the recent past. I think in the absence of anomalous signal for confirming presence of phosphate or sulphate, I would prefer to assign the electron density to the one which is present in higher concentration in the crystallization drop. Just on the basis of electron density, co-ordination geometry and functional groups attached to the tetrahedral density, I assume it is very difficult to say if it is phosphate or sulphate. In your case, I would go for SO4 instead of PO4. I would also like to know other people's experiences in such cases. Regards Simanshu On Sat, Apr 10, 2010 at 10:49 AM, wtempel wrote: > Dear colleagues, > I would like to poll the community on the prevailing practice of > distinguishing between phosphate and sulfate in their structures. > Suppose all of the following apply: > 1) a well contoured tetrahedral density in your model-phased 2Fo-Fc map in > the active site of your kinase or GTPase protein. > 2) a significant, say 5*sigma, coincident peak in your model-phased > anomalous difference fourier map from data collected at a Cu rotating anode > source. > 3) The crystal grew in 2M ammonium sulfate. > Please post your answers to the list if you feel this question is of > general interest.* > Thank you for your input. > Wolfram Tempel > > *If it is not, I apologize to everyone for wasting their valuable time. > > -- Dhirendra K Simanshu Research Scholar Memorial Sloan-Kettering Cancer Center New York, NY, USA
[ccp4bb] Need help for phasing using Tantalum bromide cluster
Dear all, I am trying to phase 172 aa protein using tantalum bromide (Ta6Br12) cluster. Data belongs to space group C2221 with 4 molecules (2 dimers) in the asymmetric unit. Phenix.xtriage indicates presence of pseudo-translation (peak height= 39). I have collected data at Ta peak (1.2550 A) to a resolution of 2.9A, Ta inflection (1.2553 A) at 2.8 A using one crystal. I also collected one high energy remote (1.059 A) data at 2.6 A using another soaked crystal. All three datasets shows presence of very good anomalous signal till the highest resolution shell. Soaking with Tantalum bromide has changed the unit cell axes "a" and "b" by 4-5 A so it is no longer isomorphous with the native data (2.7 A). But since anomalous signal is very high in all these Ta soaked datasets, I have been trying to find a solution using SAD/MAD but without any success. Processing data in lower symmetry P21 and C2 also doesn't help. Another noticeable thing is. "scalepack2mtz" fails when I try to run to convert my sca file into mtz (using CTRUNCATE option ON) with error saying "Anisotropic correction failed - negative eigen value". Since finding a solution has not been possible for reasons unclear to me. I guess I am having problem because of presence of pseudo-translational symmetry in my crystal. I would be grateful for any helpful advice or suggestions in this regard. Thanks in advance! Regards Dhirendra
Re: [ccp4bb] topology diagram
Hi Neeraj, CCP4 has a program which allows one to draw topology diagram manually...it's easy to learn and use. http://stein.bioch.dundee.ac.uk/~charlie/software/topdraw/ There is another program called "TOPS" (website is currently under maintenance) which generates topology diagram according to your pdb file. http://www.tops.leeds.ac.uk/ Hope it helps! Simanshu On Wed, Jun 11, 2008 at 11:07 AM, Neeraj <[EMAIL PROTECTED]> wrote: > Hi all, > wondering if anyone knows of a user friendly and esy to use program for > generating topology diagrams for proteins. Any help would be very useful to > me. > > thanks, > Neeraj > > -- > Neeraj Kapoor > TPCB Graduate Fellow > Sakmar Lab/ Molecular Biology & Biochemistry > The Rockefeller University > 1230 York Avenue, RRB 510 > New York, NY 10021 > lab.1.212.327.8284:fax.7904 > mobile: 917.535.2030 > http://www.rockefeller.edu/labheads/sakmar/sakmar-lab.html > -- Dhirendra K Simanshu Research Fellow Memorial Sloan-Kettering Cancer Center New York, NY, USA
