BAGIM is an active community of Boston area scientists bringing together people from diverse fields of modeling and informatics to impact life and health sciences. BAGIM strives to create a forum for great scientific discussions covering a wide range of topics including data management, visualization, computational chemistry, drug discovery, protein structure, molecular modeling, structure-based drug design, data mining, software tools, and the sharing of goals and experiences. Our community is made up of participants from academia, government, and industry whose goal is to engage in the discussion of science involving a synthesis of theory and technology. Discussions sponsored by BAGIM are targeted to the needs and interests of informatics scientists, computational chemists, medicinal chemists, and statisticians. BAGIM also provides opportunities for networking within these disciplines as well as an arena for the dissemination of information of specific interest to the membership.

Thursday, April 30, 2020


We had a very successful virtual event tonight discussing the computational impact on the COVID-19 efforts. After this event, we received this letter from Rommie Amaro of UCSD (a panelist at tonight's event and former mentor of mine).

Dear BAGIM Community,

I want to bring your attention to a new resource to help coordinate the CADD community on opportunities to contribute to COVID-19 research on potential new therapies and COVID-19 biology:

The COVID-19 Molecular Structure and Therapeutics Hub [http://covid.molssi.org] is an open data repository where biomolecular scientists can gather and disseminate critical information on the community’s efforts in targeting COVID-19. The main goals of the Hub are to provide a central resource for researchers in CADD, drug discovery, molecular modeling, and molecular simulation to not only share their efforts, but benefit from the intermediate or end products of others contributing to various aspects of COVID-19 research and drug discovery.

The COVID-19 Molecular Hub organizes

Therapeutic opportunities (such as key target proteins and binding sites)
Structural data (highlighting structures particularly suited to particular therapeutic opportunities)
Structural models (suitable for CADD or biomolecular modeling purposes, often correcting significant modeling issues in the original structural data)
Simulation data and ensembles associated with these structures and models
Molecules and bioassay data of note (such as known inhibitors, inhibitors of related proteins, and molecules with available bioassay data)
We are calling on the CADD and biomolecular modeling communities currently working on COVID-19 (or interested in doing so) to help by contributing new information about structures, models, simulations, and molecules, or joining in on data curation and review teams in areas of their expertise. New contributions can easily be made via pull requests to the GitHub repository by following the instructions on the Contributions page.
BAGIM will have so much to offer!  Please join us in this effort.
Best wishes,
Rommie Amaro

Wednesday, April 22, 2020

BAGIM (Virtual) Event: COVID-19 Panel

On April 30 at 7PM, BAGIM (the Boston Area Group for Informatics & Modeling) will be holding a virtual panel discussion covering open science and accessible tools with a focus on the search for COVID19 therapies. This global crisis has galvanized researchers around the world towards open, cooperative research. Resources such as CPU clusters enabling long timescale molecular dynamic simulations, machine trained retrosynthetic analyses to help pick realistic molecules, and structural biology results released as soon as they are refined are available to help apply decades of science and the imagination and skills of thousands to this world problem. If you wish to contribute but don’t know how, or simply wish to better understand the open science behind this global effort, we invite you to attend this first virtual BAGIM meeting. Please do not publicize or share the Zoom links. Attendees are asked to keep microphones on mute. We suggest using the ‘speaker’ view to follow the discussion from our panel.

Questions/comments will be moderated for our panel via the Zoom chat function.

To mark this first venture into BAGIM online events, we will be doing a ‘virtual selfie’ of the meeting at the end of the event so have your laptop camera & virtual backgrounds at the ready.

BAGIM April Online (Zoom) Event: Open Science and the COVID19 efforts

When: Apr 30, 2020 07:00 PM Eastern Time (US and Canada)

You must register in advance for this meeting. Please see the BAGIM Meetup for more information.

In lieu of the social hour that BAGIM normally runs we will be making a donation to Restaurant Strong, a Massachusetts charity supporting restaurant workers.

BAGIM greatly appreciates the continued support of our corporate sponsors.

Our panelists are:

Rommie Amaro - UCSD Professor, Computational Chemist & Biophysicist, Multiscale modeler

Rommie E. Amaro is a professor of chemistry and biochemistry and the director of the National Biomedical Computation Resource at the University of California, San Diego. Her research focuses on development of computational methods in biophysics for applications to drug discovery. She recently co-authored an open letter in J.Chem. Info & Model signed by 200 scientists to openly share MD methods and results on covid19 related proteins. https://en.wikipedia.org/wiki/Rommie_Amaro

Aled Edwards - Professor, University of Toronto

Professor at U. Toronto with cross appointments to Oxford and McGill, Senior Ashoka Fellow, Director of the Structural Genomics Consortium. Aled has published over 200 papers and his teams have contributed over 4,000 structures into the Protein Data Bank. Aled is a pioneer of open science and has founded several drug discovery companies with open science principles, including Affinium and M4K Pharma. Most recently, the SGC has partnered with READDI to help prepare for future pandemics. https://en.wikipedia.org/wiki/Aled_Edwards

Michael LeVine - Senior Scientist DE Shaw Research

Michael is a member of the Chemistry, Biology, and Drug Discovery team at D. E. Shaw Research, where his work focuses on macromolecular complexes and the mechanisms by which their association can be modulated. Prior to joining D. E. Shaw Research, Michael was a faculty in the Institute for Computational Biomedicine and the Department of Physiology and Biophysics at Weill Medical College of Cornell University.