About BAGIM

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.

Tuesday, July 14, 2020

BAGIM (Virtual) Event: Clayton Springer

Join us on July 28th at 6:00 pm for a seminar by Clayton Springer entitled “Self Driving Chemical Space Exploration.” Clayton Springer is in the Computer-Aided Drug Design group at Novartis.

He graduated with a B.S. in Chemistry and a minor in Math from Penn State, where he was introduced to applying computers to chemistry in Kennie Merz’s group. From there, he earned his PhD with Martin Head-Gordon at UC Berkeley in the Chemistry department. He did his postdocs at Sandia National Labs with Diana Roe and at UCSF with Fred Cohen.

At Novartis, he provides medicinal chemistry-based support of projects and technology development. His disclosed project work includes: Selective Estrogen Degraders (SERD); BCL-2; hERG inhibition; Matrix Metalloproteinase; Protein Kinase D; and Aldosterone Synthase.

On the technology side, he has been involved in Molecule Matched Pairs (MMP) and machine learning on ADMET -- specifically hERG, Human Serum Albumin (HSA), and Volume of Distribution. He was part of the team that developed Novartis’ internal med-chem productivity tool called Focus.

His recent activities in library design led him to the topic for today’s talk on “Self driving chemical space exploration.”

You must register in advance for this Zoom meeting via Meetup. All registered members will receive the link in advance.

Friday, May 1, 2020

DE Shaw Simulation Data and Github link- COVID19 Panel

Dear BAGIM Community,
Last night, we held our first-ever virtual event. Panelist, Michael LeVine, from DE Shaw Research, has forwarded links to access their simulation data, Github, and information to access Anton2.

Our simulation data and software can be found here:
Our Github, which includes our software msys, viparr, and our force fields, is here:
Information for getting access to the Anton2 machine at the Pittsburgh Supercomputing Center can be found here:
If there are any questions, please email us at sarscov2@DEShawResearch.com!
Thanks again everyone!
Michael

Thursday, April 30, 2020

Call-to-Action

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.

Tuesday, February 4, 2020

BAGIM Event: Anthony Nicholls

Please join us on Wednesday, Feb 12th for a talk by Anthony Nicholls, the President and CEO of OpenEye Scientific Software, entitled "Is your AI telling you anything you don't already know?". This event will be held at 6 pm at Le Meridien.

Originally from Plymouth, England, home to what used to be one of the worst soccer teams in the nation, Ant studied Physics at Oxford after which, looking for something different, he joined the Institute for Molecular Biophysics at Florida State University. There he studied quantum dispersion of excitations in biological systems with William Rhodes and football with Bobby Bowden. He earned his Ph.D. in biophysics in 1988 and began a post-doc with Barry Honig at Columbia University, New York. There, he re-wrote the electrostatics program DelPhi and wrote the widely-used graphics software GRASP. Owning and controlling rights to neither, he listened to the wisdom of Dave Weininger, founder of Daylight C.I.S., and left Columbia in 1997 to found OpenEye in Santa Fe, New Mexico. His chief desire is to have the work ethic of his father who, in 1996, retired as the longest serving postman in England (48.5 years). Please visit his blog “Ant’s Rants” at https://www.eyesopen.com/ants-rants/author/anthony.

Friday, December 20, 2019

Correction: BAGIM Event: Andrew Kernytsky

Please join us in the New Year for an amazing talk by Andrew Kernytsky entitled "Predicting and Detecting CRISPR Edits: On Target and Off."

Andrew Kernytsky heads up the Computational Biology and Genomics work at CRISPR Therapeutics by staring at edited DNA sequencing data and occasionally making some sense of it. Previously, he brought order to a swarm of cancer genomics data at Agios Pharmaceuticals and saw how it factored into metabolic pathways and drug targets.
Previously, Andrew dove into next-generation sequencing at the Broad Institute of MIT and Harvard. There, he contributed to the creation of a leading system for detecting DNA variants (SNPs and short indels) as well as GATK, a generalized toolkit for analyzing massive genomic data. Some key applications of this toolkit that Andrew has led or contributed to include: detecting de novo mutations in sequenced mother-father-child trios, detecting systematic errors in sequencing data, creating tools that decrease the negative downstream effects of these errors, and optimizing the protocols by which sequencing is targeted to specific areas of the genome.
Before joining the Broad, Andrew completed his Ph.D. at Columbia University in the Burkhard Rost Lab. There, he used genetic algorithms to select combinations of features from a complex space in order to predict protein function. Andrew’s undergraduate work included majors in Chemistry and Biochemistry at La Salle University. During that time, he had the opportunity to work extensively with custom microarray gene expression platforms and Affymetrix arrays at Rhone-Poulenc Rorer and Merck Research Labs. In this work, Andrew split his time between doing laboratory research and computational data exploration and tool development.

This event will be held on Thursday, January 16th, 2020 at 6:00pm at RelayTX.

Please note, this event is capped at 60 people. In order to attend, we need full names for the check list. No one will be admitted after 6:15. Please update your Meetup with your full name or email bagimcommunications@gmail.com.

Additionally, I would like to sincerely apologize for the confusion. The previous announcement was made in error, and was a result of a misread email.

The entire BAGIM team thanks you all for your continued support and for your understanding.

Happy Holidays

Tuesday, November 12, 2019

BAGIM Event: Rebecca Swett

Please join us as we hear an amazing talk by Rebecca Swett entitled "Effective Simulations, Effective Team."

This event will be held on Thursday, November 21st at 6:00pm at Novartis.

Dr. Swett graduated from Wayne State University in Detroit, where she applied molecular dynamics to the development and optimization of covalent inhibitors of the Clostridium Difficile toxins, and developed methods to apply interference in protein-protein recognition as a mechanism of inhibition, leading to her first patent. Additionally, she developed software connect genotypes to phenotypes by gene region of interest, in a hypothesis-driven manner and validated the results with simulations and in vitro experiments. She then completed a postdoc at Novartis with an academic mentor at Stanford. Here, she worked on applying ultra-fine print molecular dynamics to the use of solvation in lead optimization, application of Markov State Modeling to the identification of targetable metastable protein states for the development of flu treatments, and developed predictive models to discriminate between ligand effects on correlated protein motions in high throughput MD. She currently is at Vertex Pharmaceuticals where she uses an array of ligand and structure based methods, as well as predictive modeling and molecular dynamics, to pursue treatments for Cystic Fibrosis and other targets