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Scientist position at AbbVie
by Longenecker, Kenton L 10 Jan '17

10 Jan '17

Hi - Please see the following job opportunity below and find full description to apply at: http://abbvie.taleo.net/careersection/jobdetail.ftl?job=1608252&lang=en Senior Scientist II, Structural Biology-1608252 AbbVie (NYSE:ABBV) is a global, research-based biopharmaceutical company formed in 2013 following separation from Abbott Laboratories. The company's mission is to use its expertise, dedicated people and unique approach to innovation to develop and market advanced therapies that address some of the world's most complex and serious diseases. AbbVie employs approximately 28,000 people worldwide and markets medicines in more than 170 countries. Description The Protein Crystallography Group at AbbVie Headquarters in Lake County, Illinois is seeking a highly motivated scientist to join our Structure-Based Drug Discovery team. The ideal candidate should have extensive hands-on experience in modern X-ray Crystallography techniques and computational methods of molecular structure analysis. As part of multidisciplinary teams, the Senior Scientist will utilize fragment-based strategies to identify ligands and provide insight to advance drug discovery targets through structure-based design. The successful candidate will contribute to drug discovery projects across the portfolio of AbbVie interests that also include therapeutic antibodies and novel biologics. ________________________________ Kenton Longenecker, Ph.D. Principal Scientist AbbVie R&D Discovery, DCAT Structural Biology 1 N. Waukegan Road, AP10-LL North Chicago, IL 60064 OFFICE 847-938-1428 EMAIL kenton.longenecker(a)abbvie.com<mailto:%[email protected]> abbvie.com<http://www.abbvie.com> This communication may contain information that is proprietary, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any other dissemination, distribution, use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. ________________________________

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Academic position in glycoscience at The University of York
by Jon Agirre 09 Jan '17

09 Jan '17

Not to be confused with our previous job posting - please note the earlier deadline (5th of February) for this one! The Department of Chemistry at The University of York is seeking to appoint a high-calibre researcher in glycoscience with a clear vision to lead their own programme of excellent research, which will complement that of Professor Gideon Davies, FRS FMedSci and other members of the York Structural Biology Laboratory (YSBL). The role is available at any level and we welcome interest from talented academics with an impressive research profile appropriate to the level of application and a collegiate approach to their work. We would particularly welcome applications from researchers with a track record in chemical biology approaches to mammalian glycoscience; preferably with biomedical aspects. You will join a department renowned internationally for its research. Combined with a dedication to high-quality teaching and excellent student satisfaction, we are recognised consistently for our family-friendly policies and are proud of our Athena SWAN Gold Award. Key Requirements (viewed relative to the level of post applied for – see candidate briefs for more details): - PhD in a Chemical or Biochemical Science - Demonstrated expertise in a field/fields central to glycoscience - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to define, lead, manage and attract funds for research, operating across disciplinary boundaries - Experience of and commitment to teaching and learning at undergraduate level. - Demonstrable capacity for creative thinking and planning - Substantial recent publication record in leading peer-reviewed journal - Evidence of national and/or international collaboration More information: https://jobs.york.ac.uk/wd/plsql/wd_portal.show _job?p_web_site_id=3885&p_web_page_id=297414 Deadline for applications: 05/02/2017 -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ +44 (0) 1904 32 8270

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Academic position in cryoEM at The University of York
by Jon Agirre 09 Jan '17

09 Jan '17

The Department of Chemistry at The University of York is seeking to appoint a high-calibre researcher in cryo-electron microscopy, with a clear vision to lead their own programme of excellent research within the York Structural Biology Laboratory (YSBL). Your research will complement the X-ray crystallography and NMR techniques currently used in the YSBL, and will bridge the gap between X-ray work and the optical microscopy in the Biology Technology Facility. The role is available at any level and we welcome interest from talented academics with an impressive research profile appropriate to the level of application and a collegiate approach to their work. You will be a dynamic research leader with a consistent track record in the application of cryo-electron microscopy to challenging biochemical/biological problems. We welcome applications from researchers with an interest in diverse areas of structural and cell biology, with particular interest in those working on mammalian systems. You'll join a department renowned internationally for its research. Combined with a dedication to high-quality teaching and excellent student satisfaction, we are recognised consistently for our family-friendly policies and are proud of our Athena SWAN Gold Award. Key requirements: (viewed relative to the level of post applied for – see candidate briefs for more details): - PhD in Chemical, Biochemical or Physical Sciences - Specialist knowledge in cryo-electron microscopy - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to define, lead, manage and attract funds for research, operating across disciplinary boundaries - Experience of and commitment to teaching and learning at undergraduate level. - Demonstrable capacity for creative thinking and planning - Substantial recent publication record in leading peer-reviewed journals - Evidence of national and/or international collaboration More information: https://jobs.york.ac.uk/wd/plsql/wd_portal.show _job?p_web_site_id=3885&p_web_page_id=297412 Deadline for applications: 12/02/2017 -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ +44 (0) 1904 32 8270

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Multiple positions in Buffalo NY
by Edward Snell 06 Jan '17

06 Jan '17

Dear All, Just a reminder for those that may have missed it over the holidays. We have multiple positions for structural biologists in Buffalo NY. Please let anyone who may have an interest know of these opportunities. The first is with the Hauptman-Woodward Medical Research Institute: The Hauptman-Woodward Medical Research Institute (hwi.buffalo.edu) operates the High-Throughput Crystallization Screening Center providing crystallization and characterization services to the community at very competitive cost (www.getacrystal.org). A Ph.D. level research scientist position (post-doctoral or junior researcher) is available within the Center to guide operations on a daily basis, move research capabilities into production, and to help set the direction of the Center for the future. There is strong potential for both scientific growth and growth of responsibility. The candidate would be expected to have demonstrated expertise and productive research in the area along with appropriate publications. In addition to crystallization knowledge, experience with structural biology techniques in general is desired. Computational experience is a plus. The candidate should gave excellent communication, reading, writing, and presentation skills. They should be able to be a representative of the Center in the scientific community. They should have a good interpersonal skill set and be able to work with a diverse group. Evidence of seeking their own research funding would be viewed as a strong positive and the position would encourage the development of capabilities through active research efforts and collaboration. The Center interacts with both academia and industry and provides some crystallization screening services for a growing Gene to Structure company, HarkerBIO, (www. harkerbio.com). Collaborative possibilities are possible in this area. Research facilities at the Center include liquid handling robots, in-house developed plate imaging capabilities, SONICC and UV analysis, and X-ray analysis. The Center is well connected to several synchrotron facilities. A sophisticated computational infrastructure is in place. In both the X-ray and computational side, research advances are ready to be implemented into the Centers capabilities. The Hauptman-Woodward Medical Research Institute is 60 years old and based in Buffalo New York. It is at the center of a rapidly expanding medical campus. Good benefits are provided and the cost of living in the area is very competitive. For those with a focused research interest, the Institute is located adjacent to high-end computer facilities, a Comprehensive Cancer Center, a new Medical School under construction, and multiple biotech startup companies. Collaborative efforts with academic and industrial collaborators are strongly encouraged and aided by an umbrella organization on the campus. The Hauptman-Woodward Medical Research Institute, Inc. as an equal opportunity employer, extends employment opportunities to qualified applicants and employees on a non-discriminatory basis without regard to race, color, sex, creed, age, religion, national origin, marital status, veteran status, sexual orientation, genetic predisposition, carrier status, or disability that would prevent the performance of the essential requirements of the job with or without a reasonable accommodation in compliance with the appropriate New York State and Federal laws, or any other legally protected characteristics. This policy applies to all conditions and terms of employment. Formal applications should send a cover letter and resume along with three contacts for references to opportunity(a)hwi.buffalo.edu. The position is available in the New Year and will be open until filled. And on behalf of Artem Evdokimov, HarkerBIO CEO, the other positions are with a company called HarkerBIO housed in the Hauptman-Woodward Medical Research Institute building: HarkerBIO is hiring two *Research Scientist - Structural Biology * positions. Desired qualifications are quite broad, but can be summarized as follows: 1) someone who is a start-up enthusiast, not afraid of a challenge and has both the desire to innovate in science and the ability to do so. A PhD in related area is a plus, however we would consider qualified M.Sc. candidates. 2) someone with a relevant experience in at least 70% of the gene to structure 'process' - in other terms, the candidate is able to perform literature research, design clones, clone, express, purify, crystallize and solve structures -- or at least a good chunk of the above. Ideally someone with experience in mammalian and/or insect cell expression, and/or membrane protein work. 3) a scientist with a reasonably rounded skill set in biophysical characterization of macromolecules (SPR, DSF, anSEC/MALS, and so forth) 4) deep interest in developing structure-related technologies (e.g. expression systems, crystallization research, etc.). Desire and ability to participate in internal research projects. 5) high work ethic, impeccable documentation abilities, sense of humor 6) committed to relocating to Buffalo, NY HarkerBIO offer: Competitive salary (commensurate with experience) and full benefits Energetic and friendly work environment Coverage of reasonable relocation expenses for highly qualified candidates Co-location with a nonprofit research institute (HWI) and participation in the thriving research community at the Buffalo-Niagara Medical Campus HarkerBIO is an EO/AA employer. Please direct your inquiries to careers(a)harkerbio.com<mailto:[email protected]>. Note that for both positions, applications should be addressed to the emails given in the position descriptions. Happy New Year, Eddie Edward Snell Ph.D. President and CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 hwi.buffalo.edu Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu [cid:[email protected]] Heisenberg was probably here!

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Phenix.model_vs_data - Rfree difference
by Luca Pellegrini 03 Jan '17

03 Jan '17

Hello, I am trying to find out the reason for a large R-free difference that I am getting between phenix.refine and phenix.model_vs_data: phenix.refine R-work/R-free 0.1702/0.1974 phenix.model_vs_data R-work/R-free 0.1728/0.1795 Initial refinement was using the intensities in an XDS_ASCII.HKL dataset, followed by a few refinement cycles against the same dataset, but using amplitudes calculated in Aimless, with the ‘skip scaling just merge’ option and keeping the FreeR reflections. When I checked R-free values for the last refinement run before the conversion, there was no large discrepancy: phenix.refine R-work/R-free 0.1720/0.2086 phenix.model_vs_data R-work/R-free 0.1715/0.2080 Can anyone please advise? Apart from this, refinement went well - both the 1.9A map and the model look fine. Thanks for the help & happy New Year, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

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Postdoctoral Fellow Position at US MHRP, WRAIR
by gjoyce＠hivresearch.org 30 Dec '16

30 Dec '16

Dear All, A postdoc position is available in a newly formed Structural Biology Section, part of the US Military HIV Research Program, WRAIR in Silver Spring, Maryland, USA. The position involves the application of structural biology to understanding viral glycoproteins and the immune response following vaccination or natural infection. Interested and qualified individuals can apply through the following official link at Job ID: 212324 at the Henry M Jackson Foundation careers website: http://www.hjf.org/careers/open-jobs. Applicants must be US citizens or have lived in the US for at least 3 consecutive years. Please feel free to contact me at gjoyce(a)hivresearch.org if you have any questions. Best wishes, Gordon HJF is seeking a Postdoctoral Fellow to support the Military HIV Research Program (MHRP) located at the Walter Reed Army Institute of Research (WRAIR) in Silver Spring, Maryland. The incumbent will be responsible for initiating and carrying out scientific projects, under the supervision of senior scientists and in collaboration with other research scientists. The position involves the characterization of the humoral immune response to HIV-1 infection and HIV-1 vaccines using X-ray crystallography. The incumbent will be responsible for conducting and publishing research in HIV structural biology. The incumbent will work within a multidisciplinary environment consisting of military, government, academic, and international collaborators. Responsibilities: Conducts independent research and learns techniques required to conduct the research. Assists in designing, developing, executing, and implementing scientific research and/or products. Develops a thorough understanding of the scientific literature relating to the research topics. Collects and handles samples and keeps detailed inventory and records of experiments by maintaining up to date, clear, and accurate laboratory notebooks. Executes projects related to biochemical and structural characterization of antibodies, vaccine candidates and their complexes. Analyzes experimental data, applying relevant statistical and bioinformatic models. Presents data at scientific meetings and publishes original research in peer-reviewed journals. Assists with training laboratory staff and collaborates with labs within and outside of MHRP. Follows all MHRP and WRAIR safety procedures and completes required training in a timely manner. Performs other duties as assigned. Required Knowledge, Skills, and Abilities: PhD in structural biology or related area with significant experience in X-ray protein crystallography. Knowledge of appropriate scientific area; ability to analyze and interpret data. Experience and proficiency in protein purification, protein characterization, X-ray crystallography including up-to-date knowledge of relevant programs including CCP4, and Phenix packages. Experience with project planning, implementation, and data analysis. Experience in presenting at scientific meetings and writing manuscripts for scientific journals. Practical knowledge of electron microscopy, molecular modelling or structure-based mutagenesis and design is an advantage. Minimum Education/Training Requirements: Ph.D. in structural biology, molecular biology, immunology, microbiology, biochemistry or related discipline. Minimum Experience: 0-2 years of postdoctoral experience Physical Capabilities: Long periods of standing and sitting; intricate work with hands; carrying of light and moderately heavy laboratory equipment. Job performance requires movement around and between several laboratories, and long periods of sitting at laboratory bench. Fine motor coordination in manipulation of laboratory materials is essential. Supervisory Responsibilities/Controls: May provide guidance to laboratory staff. Work Environment: Laboratory environment; may require working evenings and weekends. The incumbent will be expected to practice safe handling of hazardous chemicals. This laboratory is densely populated and requires good interpersonal skills for effective job performance. This position requires working and occasional travel to US synchrotron facilities. This Postdoctoral Fellow will support the US Military HIV Research Program, located at The Walter Reed Army Institute of Research (WRAIR) in Silver Spring, MD. HJF is an equal opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, or protected veteran status. Any qualifications to be considered as equivalents, in lieu of stated minimums, require the prior approval of the Director of Human Resources. M. Gordon Joyce, Ph.D. Chief, Structural Biology Section The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF) US Military HIV Research Program (MHRP) Walter Reed Army Institute of Research (WRAIR) 1N33, 503 Robert Grant Ave, Silver Spring, MD 20910 Office: 301-319-7528 Cell: 240-672-4311 gjoyce(a)hivresearch.org Web: www.hivresearch.org Facebook: www.facebook.com/hivresearch YouTube: www.youtube.com/mhrpvideos Twitter: www.twitter.com/mhrpinfo The U.S. Military HIV Research Program (MHRP), centered at the Walter Reed Army Institute of Research (WRAIR), is an international HIV vaccine research program that successfully integrates HIV/AIDS prevention, care and treatment.

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Spring 2016 MicroED workshops at Janelia Research Campus
by Hattne, Johan 23 Dec '16

23 Dec '16

Due to high demand, two back-to-back MicroED workshops will be held at Janelia Research Campus (Ashburn, VA) in the spring. The workshops are hosted by Tamir Gonen and will have the same content. Accepted participants will be assigned by the organizers to one or the other (not both). May 21-24 and May 24-27, 2017 MicroED is a cryoEM method that uses electron diffraction to facilitate structure determination from sub-micron sized 3D crystals, eliminating the need to grow large crystals. MicroED uses equipment and procedures that are standard on many cryoTEM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To facilitate the widespread use of MicroED, we are offering these workshops to teach microscopists how to perform the technique and adopt it at their own institutions. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Applicants must register and submit a brief statement on why they wish to participate, via our online registration system. https://conference.janelia.org Please note that this system is designed to collect abstract information for presentations. Please write your statement of interest in the "abstract" field, put your name in the "author" field, and put "n/a" in the "presentation title" and "keyword" fields. Space in these workshops is limited. The application deadline is February 10, 2017. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

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Job opportunity - Structural Biology GSK Vaccines
by Enrico Malito 22 Dec '16

22 Dec '16

Dear phenix community, The Structural Biology Lab at GSK Vaccines, Rockville, MD, USA, is seeking a candidate for a Scientist/Senior Scientist position (Job ID: 148543, hiring managers: Enrico Malito, Matthew Bottomley). We offer outstanding opportunities and compensation to outstanding candidates. Anyone interested to apply can do so by visiting this link: https://careers.peopleclick. com/careerscp/client_gsk/external1931/en-us/gateway.do? functionName=viewFromLink&jobPostId=323652&localeCode=en-us (Please note that this may wrap to another line of text; you may need to copy and paste the entire URL into your browser window). Applications will be accepted only through the page at the link above. Examples of relevant recent publications: - Rappuoli et al 2016. Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design. http://dx.doi.org/10.1084/jem.20151960 - Chandramouli et al 2015. Structure of HCMV glycoprotein B in the postfusion conformation bound to a neutralizing human antibody http://dx.doi.org/10.1038/ncomms9176 - Ciferri et al 2015. Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies http://dx.doi.org/10.1371/journal.ppat.1005230 - Malito et al 2015. Protein Crystallography in Vaccine Research and Development. http://dx.doi.org/10.3390/ijms160613106 Yours sincerely, *Enrico Malito, PhD* *Lab Head of Structural Biology and BiophysicsGSK VaccinesPreclinical R&D USGSK Vaccines14200 Shady Grove Road, Rockville MD 20850, USA*

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alingments in mr_rosetta
by Kajander, Tommi A 21 Dec '16

21 Dec '16

Hi, I am wondering about the alignment of sequence and PDB model in mr_rosetta - the program seems to complain if the sequences dont exactyl match - so is this really the case? (I have an initial model from autobuild with some fragments that do not have fully correct sequence - hence it doenst exactly match with the original sequence of the protein). Does it have to? Or should there be a way around it? also the command file examples online e.g. : phenix.mr_rosetta \ seq_file=seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ already_placed=True \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=2 \ space_group=p212121 \ use_all_plausible_sg=False \ nproc=200 \ group_run_command=qsub when using the command file all the commands are not recognized for some reason (running on a mac with bash shell) e.g. rescore_mr.relax=False, same with fragment files… not quite sure what the problems is there, probably something trivial. -if i just enter them on the command line it works. Thanks, Tommi

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Error from f_model_all_scales.py
by John Bruning 20 Dec '16

20 Dec '16

Hi (Pavel), I have a dataset (P31) which I am processing with the pairwise combinations of reindexing operators (4 incl. no reindexing therefore h,k,l) and twin laws (4 incl. no twinning as h,k,l). While some of these combinations are fine during refinement (Vers 1.11.1), for some combinations I get the following error, which ultimately kills the refinement. Thanks in advance and apologies if I am missing something stupid. Incidentally, a different dataset seems to tolerate all combinations. *approx_equal eps: 1e-05* *approx_equal multiplier: 10000000000.0* *0.512707954357 approx_equal ERROR* *0.514972857238 approx_equal ERROR* Traceback (most recent call last): File "/Applications/phenix-1.11.1-2575/build/../modules/phenix/ phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/command_line.py", line 154, in run call_back_handler=call_back_handler) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/driver.py", line 1529, in run call_back_handler = call_back_handler).result File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/strategies.py", line 121, in __init__ log = log) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/fmodels.py", line 159, in run fmodel.update_solvent_and_scale(initialise=True) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/twinning/twin_f_model.py", line 797, in update_solvent_and_scale params=params, log=log, apply_back_trace=apply_back_trace) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1457, in update_all_scales params = params, log = log, refine_hd_scattering=refine_hd_scattering) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 38, in __init__ refine_hd_scattering = refine_hd_scattering, log = log) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 61, in compute refine_hd_scattering = refine_hd_scattering) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 329, in update_solvent_and_scale_twin * assert approx_equal(self.r_all(), o_kbu_sol.r(), 1.e-5)* *AssertionError*

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