- compbio-allhands@cgl.ucsf.edu - RBVI Mailing Lists

[Compbio-allhands] TODAY! 4 PM in GH Auditorium! Peter Kollman Lectureship with Ken Dill, PhD
by Flowers, Nicole 05 May '22

05 May '22

PETER A. KOLLMAN LECTURESHIP Ken Dill Stonybrook Thursday, May 5, 2022 4:00 PM Brian Shoichet, Host Genentech Hall Byers Auditorium Livestream: http://tiny.ucsf.edu/Y5D1RO Reception to follow in Genentech Hall 1st Floor Atrium

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[Compbio-allhands] Register for Advanced Cytoscape Automation
by Zainab Yusufsada 04 May '22

04 May '22

GLADSTONE DATA SCIENCE PROGRAM*Advanced Cytoscape Automation* May 10, 2022 • 1–4pm Alex Pico Online Join this workshop if you’re already using R or Python and are curious about network analysis and visualization. You’ll learn how to integrate Cytoscape’s network capabilities into your bioinformatic workflows. LEARN MORE AND REGISTER <https://gladstone.org/events/advanced-cytoscape-automation-0>

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[Compbio-allhands] 5/5/22 Peter Kollman Lectureship with Ken Dill, PhD
by Flowers, Nicole 29 Apr '22

29 Apr '22

PETER A. KOLLMAN LECTURESHIP Ken Dill Stonybrook Thursday, May 5, 2022 4:00 PM Brian Shoichet, Host Genentech Hall Byers Auditorium Livestream: http://tiny.ucsf.edu/Y5D1RO Reception to follow in Genentech Hall 1st Floor Atrium

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[Compbio-allhands] Fwd: question - re: co-crystal structure ligand based design
by Brian Shoichet 28 Apr '22

28 Apr '22

FYI ---------- Forwarded message --------- From: Robert Batey <rob.batey(a)utoronto.ca> Date: Thu, Apr 28, 2022 at 8:08 AM Subject: Re: question - re: co-crystal structure ligand based design To: Brian Shoichet <bshoichet(a)gmail.com> Dear Brian Hope that you are well. I don’t know whether you saw this, but we have a full-time tenure stream position in the area of computational chemistry applied to medicinal chemistry and chemical biology. The appointment is at the rank of Associate Professor or Professor with an expected start date of July 1, 2023. The posting for this position can be found here: https://jobs.utoronto.ca/job/Toronto-Associate-ProfessorProfessor-Computati…. All application materials, including reference letters, must be received by *May 17, 2022.* Successful candidates may also be nominated for a *Canada Excellence Research Chair <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cerc.…>* in Medicinal Chemistry, AI/Machine Learning and Computational Chemistry, Chemical Biology valued at $1 million/year for 8 years. The Canada Excellence Research Chairs (CERC) program is intended to support world‑renowned researchers and their teams in establishing ambitious research programs at Canadian universities. Nominees to the CERC opportunity will be internationally leading researchers whose proposed research program aligns with one or more of the *Government of Canada’s Science, Technology and Innovation priority areas <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cerc.…>*. The labs would be primarily located in the Princess Margaret Cancer Centre. I wonder whether you know anyone who you think might be appropriate? Would you share this opening with your networks? Let me know if you have any questions. Cheers Rob *From: *Undisclosed Recipients <rob.batey(a)utoronto.ca> *Date: *Wednesday, March 16, 2022 at 1:50 PM *To: *Brian Shoichet <bshoichet(a)gmail.com> *Cc: *Daniel Erlanson <erlanson(a)gmail.com> *Subject: *Re: question - re: co-crystal structure ligand based design Dear Brian and Dan (nice to be virtually acquainted btw, I enjoy the blog) Thanks for this – very helpful, and two interesting examples. In the case we have the two orientations are linked by a single bond rotation, and it enabled us to design an entirely new class of compound that allowed for both of the two orientations to be mimicked in a single compound. Cheers Rob –––––––––––––– Robert A. Batey, Ph. D. Professor and Chair Department of Chemistry <https://www.chemistry.utoronto.ca/>, LM 151 University of Toronto <https://www.utoronto.ca/> 80 St. George St., Toronto, ON CANADA, M5S 3H6 Chair's office: 416-978-3566; fax: 416-978-1631 Web: http://www.chem.utoronto.ca/staff/RAB/index.html Linked-In: https://www.linkedin.com/in/robert-batey-156221a2 I wish to acknowledge this land on which the University of Toronto operates <https://indigenous.utoronto.ca/about/land-acknowledgement/>. For thousands of years it has been the traditional land of the Huron-Wendat, the Seneca, and the Mississaugas of the Credit. Today, this meeting place is still the home to many Indigenous people from across Turtle Island and we are grateful to have the opportunity to work on this land. –––––––––––––– *From: *Brian Shoichet <bshoichet(a)gmail.com> *Date: *Saturday, February 5, 2022 at 8:47 PM *To: *Undisclosed Recipients <rob.batey(a)utoronto.ca> *Cc: *Daniel Erlanson <erlanson(a)gmail.com> *Subject: *Fwd: question - re: co-crystal structure ligand based design You don't often get email from bshoichet(a)gmail.com. Learn why this is important <http://aka.ms/LearnAboutSenderIdentification> Dear Rob, I rec'd these references from Dan Erlanson, copied. They speak to your case, I think you'll find them useful in framing your cool story. Brian ---------- Forwarded message --------- From: *Daniel Erlanson* <erlanson(a)gmail.com> Date: Sat, Feb 5, 2022 at 7:59 AM Subject: Re: question - re: co-crystal structure ligand based design To: Brian Shoichet <bshoichet(a)gmail.com> Hi Brian, Nice to hear from you! A couple examples come to mind, though I feel like there are more: https://practicalfragments.blogspot.com/2020/05/merging-two-of-same-fragmen… <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpractical…> https://practicalfragments.blogspot.com/2013/10/fragment-merging-revisited-… <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpractical…> BTW I liked your recent SARS-CoV-2 aggregation paper - unfortunately too much crap got published in the past couple years. Cheers, Dan -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbkslab.or…>* -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://bkslab.org/>*

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[Compbio-allhands] 4/28/22 BBC Seminar with Karlene Cimprich, PhD
by Flowers, Nicole 22 Apr '22

22 Apr '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Genentech Hall Byers Auditorium Livestream: http://tiny.ucsf.edu/Y5D1RO Co-sponsored by the [cid:93c19575-2d2a-4361-a102-7fb3b8de7827] Karlene Cimprich, PhD Stanford University RNA Meets DNA: Dangerous Liaisons in the Genome April 28, 2022 L. Weinberger, host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] 4/21/22 BBC Seminar Cancelled
by Flowers, Nicole 15 Apr '22

15 Apr '22

Next week Thursday's BBC Seminar with Dr. Elizabeth Villa has been postponed. Please stay tuned for a rescheduled date. Nicole Takesono Flowers Biophysics Graduate Program Manager UCSF MC 2240 600 16th St. Genentech Hall Room N474D San Francisco, CA 94158-2517 Phone: (415) 502-6518

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[Compbio-allhands] 4/14/22 BBC Seminar with Tanja Mittag, PhD, Noon
by Flowers, Nicole 08 Apr '22

08 Apr '22

BBC Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, Noon Zoom: http://tiny.ucsf.edu/pUYmCK Please do not share this link outside of UCSF Tanja Mittag, PhD St. Jude Children's Research Hospital Protein disorder, multivalency and phase separation: Implications for biological function and disease April 14, 2022 W. Weiss, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Gladstone Center for Cell Circuitry. Subscribe to the BBC Seminar Series Calendar! Use this URL to access this calendar from a web browser.<https://urldefense.com/v3/__https://calendar.google.com/calendar/embed?src=… > Use this address to access this calendar from other applications.<https://urldefense.com/v3/__https://calendar.google.com/calendar/u/1?cid=cz… > Use this URL to view and open the calendar in iCal and/or Outlook.<https://urldefense.proofpoint.com/v2/url?u=https-3A__ucsf.us20.list-2Dmanag…> To view recorded lectures, click here: https://lecture.ucsf.edu/ets/Channel/0671978c87c64a7db9251cff75b922505f

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[Compbio-allhands] Check Out the Spring Line Up for the Gladstone Data Science Training Program
by Zainab Yusufsada 06 Apr '22

06 Apr '22

The Gladstone Data Science Training Program <https://gladstone.org/events?series=data-science-training-program> provides you with learning opportunities and hands-on workshops to improve your skills in bioinformatics and computational analysis. Join one of these upcoming workshops to gain new skills and get support with your data. Spring 2022 Series All workshops are virtual! Single Cell RNA-Seq Analysis April 15-19, 2022 Register <https://gladstone.org/events/single-cell-rna-seq-analysis-2> Statistics of Enrichment Analysis April 22, 2022 Register <https://gladstone.org/events/statistics-enrichment-analysis-0> Introductory Machine Learning for Biologists May 3, 2022 Register <https://gladstone.org/events/introductory-machine-learning-biologists-2> Advanced Cytoscape Automation May 10, 2022 Register <https://gladstone.org/events/advanced-cytoscape-automation-0> Cordially, *Zainab Yusuf Sada* | Administrative Specialist Gladstone Institute of Data Science & Biotechnology 1700 Owens Street, San Francisco, CA 94518 T 415.734.4827|zainab.yusufsada(a)gladstone.ucsf.edu

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[Compbio-allhands] Fwd: Assistant Professor position Baylor College of Medicine
by Brian Shoichet 04 Apr '22

04 Apr '22

FYI ---------- Forwarded message --------- From: Palzkill, Timothy Gerald <timothyp(a)bcm.edu> Date: Mon, Apr 4, 2022 at 8:42 AM Subject: Assistant Professor position Baylor College of Medicine To: shoichet(a)cgl.ucsf.edu <shoichet(a)cgl.ucsf.edu> Dear Brian, I hope all is well with you. My department has a tenure track Assistant Professor position available. Our specific areas of interest for this position include computer-aided drug design (CADD), molecular dynamics (MD) simulations, protein design and folding prediction, application of machine learning and artificial intelligence (AI) to improve the target identification and drug discovery process. If your trainees are in the market for a faculty job, please pass this information along. They can find more detailed info and apply via this link https://bit.ly/36oTHSp or email directly to pharmacology(a)bcm.edu . Thanks, Tim Timothy Palzkill, Ph.D. Cullen Trust for Higher Education Chair Professor and Chair Department of Pharmacology and Chemical Biology Baylor College of Medicine -- Brian Shoichet, Professor, UCSF latest science from the lab: *https://bkslab.org/ <https://bkslab.org/>*

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[Compbio-allhands] 4/7/22 Braisted Lecture with Alanna Schepartz
by Flowers, Nicole 01 Apr '22

01 Apr '22

UCSF-UCB Andrew Braisted Award Lectureship Livestream: http://tiny.ucsf.edu/Y5D1RO Alanna Schepartz, Ph.D. UC Berkeley Reimagining the Definition of a Protein Thursday, April 7, 2022 4 pm Genentech Hall Byers Auditorium UCSF Mission Bay Campus Contact: Charles Craik Sponsor: The Andrew Braisted Lecture Fund

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