August 2020 - phenixbb - phenix-online.org

map to model - DNA model building
by Manoj saxena 04 Aug '20

04 Aug '20

Hello, I am trying to fit a cryo-EM map of a DNA protein complex (3.3 A) using the map to model in Phenix 1.18.2.3874, with a DNA sequence input in fasta format and the map as a .ccp4 file. However the output model fitted in the map I am getting is many fragmented PDB files and only one chain of DNA. What is the best way to get a higher fraction of the DNA model fitted into the map, can I switch off the segmentation of map and get both strands fitted into the map. Or the only option is to manually build? Thanks for your help Regards Manoj Saxena

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Model moving out of map
by Shanti Pal Gangwar 03 Aug '20

03 Aug '20

Dear all, I am trying to refine a Cryo-EM map at a decent resolution. The model was fit into the map in chimera and refined against the same map in Real space refinement in Phenix but after the run, a significant part of the model moved out of the density. I would appreciate any suggestion/strategy to solve this issue. Thank you Shanti Pal

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Postdoc position at UT Health Science Center, San Antonio, Texas
by Yogesh Gupta 03 Aug '20

03 Aug '20

The laboratory of Dr. Yogesh Gupta at University of Texas Health Science Center in San Antonio is seeking an enthusiastic Postdoctoral Fellow to study the structure and function of nucleoproteins in infectious diseases and cancer. We combine structural biology tools (X-ray, cryo-EM, NMR) with cell-based methods to address mechanistic questions and exploit this knowledge for drug development. Please visit below websites to learn about our research program – https://www.nature.com/articles/s41467-020-17496-8 *http://ccri.uthscsa.edu/YGupta.html <http://ccri.uthscsa.edu/YGupta.html>* Preference will be given to applicants with demonstrated experience in macromolecular crystallography. Candidates are expected to possess strong organizational, interpersonal skills, and ability to work as part of a team. An ideal candidate should hold (or soon expect to hold) a Ph.D. or equivalent degree in biochemistry/biophysics/structural biology and have no more than 2 years of postdoc experience. Salary is competitive. San Antonio offers affordable cost of living and there is no state income tax in Texas. If interested in applying, please send a short description of your research accomplishments, and CV with a list of 3 references to Dr. Yogesh Gupta (email: *guptay(a)uthscsa.edu <guptay(a)uthscsa.edu>*). The Greehey Children’s Cancer Research Institute is a unique specialized cancer research center focusing on basic and translational research in childhood cancer and occupies a state-of-the-art 100,000 sq. foot research facility on the university’s Greehey Academic and Research Campus. San Antonio is the nation’s seventh largest city and is located at the edge of the beautiful Texas Hill Country. San Antonio offers a rich, multi-cultural community, affordable cost of living, excellent weather and a thriving biomedical industry.* All Postdoctoral appointments are designated as security sensitive positions. The University of Texas Health Science Center at San Antonio is an Equal Opportunity/Affirmative Action Employer including protected veterans and persons with disabilities.* Thank you very much for your time. Yogesh -- Yogesh Gupta, PhD Assistant Professor of Biochemistry & Structural Biology PI, Greehey Children's Cancer Research Institute University of Texas Health Science Center 8403 Floyd Curl Drive, San Antonio, Texas, USA 78229 http://ccri.uthscsa.edu/YGupta.html

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Fwd: Sanofi Postdoctoral Fellowship: Computational Scientist for Antibody Engineering (Greater Boston, MA)
by yanfeng zhou 01 Aug '20

01 Aug '20

If you have strong interest in one of the following areas, please continue to read and check the link for more details. 1. Developing new algorithms to revolutionize biologics discovery 2. Challenging yourself with large and unique datasets and converting your learnings to tools/products that can help patients 3. Engineering of antibody, nanobody, and other biotherapeutics modalities 4. Learning how scientists from various training backgrounds collaborate together to discover and deliver faster and better biologics treatments. The Protein Engineering group within Sanofi Large Molecule Research Department is seeking a highly talented Computational Scientist for a postdoctoral position. We use leading-edge structural biology and computational tools to support biologics project needs from Sanofi’s multi-targeting, multi-modality research pipeline. Our team has a great track record of patents and publications, including Science, Nature Cancer, and Nature Communications, in the area of biologics characterization, antibody engineering and multi-specific antibodies. This postdoc project will focus on developing a machine learning approach to predict epitope-paratope, given any antibody-antigen pair, by combining in-depth understanding of structure biology, antibody engineering, and large datasets both internally and externally. The successful candidate will be with Ph. D. degree in related area and has an advanced understanding and practical experience with developing and applying complex machine learning solutions for structural biology data. The successful candidate will gain deeper insight into drug development process and transform AI/ML algorithms into accelerating biologics discovery and development process. Application Link: https://sanofi.wd3.myworkdayjobs.com/en-US/StudentPrograms/job/Framingham-M… *About Sanofi:* Every day, Sanofi's 100,000 employees are committed to improve the lives of people around the world, with sustainable and responsible solutions and initiatives. Sanofi is recognized as one of the leading biopharmaceutical companies in the world and is pioneering innovation in biologics with the first approved nanobody drug, the first clinical stage tri-specific antibody, and a novel genetic codon expansion platform for new engineering capabilities. Details of the organization and the company’s mission and goals can be found on our website (http://www.sanofi.us/l/us/en/index.jsp). ------------------------------ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Yanfeng Zhou, Ph.D. Email: YanfengZhou.pku(a)gmail.com <yanfengzhou.pku(a)gmail.com>

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