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, November 15, 2016

BAGIM Event: Dr. Georgia McGaughey Monday December 5 at Millennium Takeda in Cambridge

Dr. Georgia McGaughey of Vertex Pharmaceuticals will present "Shaping Computational Chemistry Tools for Impact: Application of Experimental and Theoretical Methods for Orexin Antagonists" at the Millennium Takeda Oncology building at 35 Landsdowne Street in Cambridge, MA on Monday, December 5th. The presentation will begin at 6pm followed by refreshments and networking at Asgard, 350 Massachusetts Ave. Adding your full name to your RSVP  will speed security registration at Takeda.

BAGIM is sponsored by Scilligence, Silicon Therapeutics, Acellera, Cyrus Biotechnology, DNASTAR, OpenEye Scientific Software, Schrodinger, Chemical Computing Group, ARIAD Pharmaceuticals, Vertex Pharmaceuticals, the Cambridge Crystallographic Data Centre, Optibrium, Dassault Systemes, Dotmatics, LabAnswer, and ChemAxon.

BAGIM Event: Panel Discussion Exploring Careers in Computational Chemistry and Cheminformatics at Moderna November 10th

Interested in pursuing a career in computational chemistry or cheminformatics? Join us for a panel discussion by young career scientists in industry, ranging from big pharma to startups. Learn tips and tricks for successful interviewing, networking, and job hunting. Hear what it's like making the transition from academia to industry and what it's like working in the field.   A BAGIM networking event at Cambridge Brewing Company will follow the panel discussion at 7:15pm.
·  5:30-6pm -- Drinks and food
·  6-7pm -- Career panel aimed at graduate students and postdocs considering careers in comp chem
o Panelists include
§ Dr. Rebecca Swett (Vertex)
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.
§ Dr. Levi Pierce (Relay Therapeutics) 

Levi is a computer engineer who has worked in several startups spanning the fields of genomics and pharmaceutical drug design.  The combination of these two fields will usher in personalized medicine.  While at Schrodinger Inc, he was a key developer of a computational tool (Free Energy Perturbation, FEP) used to accurately predicting binding affinity of drugs in lead optimization.  He then worked at Human Longevity Inc using a variant of FEP to study drug sensitivity observed in cancer mutations obtained from next generation sequencing.  Currently he is at Relay Therapeutics where he is leveraging computational tools to develop drugs for mutations observed in patient populations.  
§ Dr. Christine Hajdin (Novartis)
Currently, Christine is an investigator in the CADD (Computer Assisted Drug Discovery) group at Novartis. Here she utilizes a mix of machine learning, informatics, programming and structure-based design to identify potential target/compound interactions.  Prior to coming to Novartis, she worked at Explorys (now IBM Watson Health) as a data scientist modeling cost reduction and risk aversion strategies.  She obtained her Ph.D. from UNC Chapel Hill in biological chemistry and undergraduate degrees in math and biochemistry from Miami University.
Moderated by Dr. Finith Jernigan, III (Silicon Therapeutics). 

Dr. Jernigan is a co-founder and chief technology officer of Silicon Therapeutics and was instrumental in developing the underlying technology INSITE. Prior to founding Silicon Therapeutics, Dr. Jernigan was at Beth Israel Deaconess Medical Center, a teaching hospital of Harvard Medical School, where his focused on identification of tool compounds using novel in silico screening approaches for targets identified by BIDMC investigators. This work, performed in the labs of Drs. Sun and Chaikof, led to the creation Silicon Therapeutics’ proprietary drug discovery platform, INSITE. Prior to that, Dr. Jernigan earned his Ph.D. in organic chemistry at the University of North Carolina at Chapel Hill in the lab of Dr. David S. Lawrence. His work at the University of North Carolina focused on the synthesis and development of fluorescent sensors of kinases and the proteasome. This work led to multiple publications in top chemistry journals, including Journal of the American Chemical Society and Angewandte Chemie International Edition. Dr. Jernigan holds a B.S. in Biochemistry from Salisbury University, a Ph.D. in Organic Chemistry from the University of North Carolina at Chapel Hill, and was a postdoctoral fellow at BIDMC/Harvard Medical School.

Thursday, October 6, 2016

BAGIM Event: Dr. Alan Rigby Tuesday October 18th starting at 6pm, Le Meridien Cambridge/MIT

Dr. Alan Rigby, CSO of Warp Drive Bio, will be presenting at Le Meridien Cambridge/MIT in the Taylor room on Tuesday, October 18th.  The talk will start at 6pm, and afterwards we will move to Meadhall at 4 Cambridge Center for refreshments.

Please RSVP early and often to help us plan the evening accurately.

BAGIM is sponsored by Scilligence, OpenEye Scientific Software, Schrodinger, Chemical Computing Group, ARIAD Pharmaceuticals, Vertex Pharmaceuticals, the Cambridge Crystallographic Data Centre, Optibrium, Dassault Systemes, Dotmatics, LabAnswer, and ChemAxon

Wednesday, September 14, 2016

BAGIM Event: Dr. Andy Maynard Sept. 26th Starting at 6pm at Vertex

Dr. Andy Maynard of Creode Analytics will present "Lead Optimization Dynamics"  on Monday, September 26th at 7 pm following refreshments at 6 pm on the 9th floor of the Vertex One building at 50  Northern Avenue, Boston.

Lead optimization (LO) is a challenging team “sport”, involving a diverse team of scientists who strive to efficiently convert early chemical starting points into mature clinical assets. Traditionally, LO has been quantified in terms of static “compound quality” endpoints, without regard to quantifying the dynamical nature of the LO process. Here, we consider LO as a process that minimizes risk, defined in simple statistical terms, to holistically visualize the trajectories of drug discovery projects as a means to objectify LO progress and to define determinants of efficiency.  In addition, LO convergence metrics are developed to facilitate comparison of project tractability (for project portfolios).

http://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.5b00948

Vertex is a short 12 minute walk from South Station via Atlantic and Northern Avenues, or take the Silver Line bus from South Station to Court House Station and cross Northern Avenue.  Parking is available in the Pilgrim Parking Fan Pier parking garage beneath the building for a flat $15 fee after 5pm.  There is also street parking with coin meters and smart meters in the area.

Security procedures and sign-in at Vertex will be accelerated by having your full name.  Please add them to your RSVP or email me your full name at bagimcommunications@gmail.com Thank you! 

BAGIM is sponsored by Scilligence, OpenEye Scientific Software, Schrodinger, Chemical Computing Group, ARIAD Pharmaceuticals, Vertex Pharmaceuticals, the Cambridge Crystallographic Data Centre, Optibrium, Dassault Systemes, Dotmatics, LabAnswer, and ChemAxon

Friday, July 22, 2016

BAGIM Event: Dr. Tzachi Pilpel August 9th starting at 5:45 pm at the Broad

Dr. Tazchi Pilpel of the Weizmann Institute will present "Revealing and Manipulating the Costs of Gene Expression" on Tuesday, August 9th at 7pm, following refreshments and networking at 5:45pm, at the Broad Institute, 415 Main St. Cambridge MA.

Dr. Pilpel's more detailed description of the talk: "Cells invest a significant amount of their energy and other resources to express their proteins. An economic strategy for gene expression would amount to an evolutionary design of genes whose proteins are expressed at a desired level but that minimize consumption of cellular resources during production. I will describe our usage of a synthetic gene approach, combined with in-lab massive competition and deep sequencing to reveal architectures of genes that evolved to minimize gene expression burden while maintaining a desired protein expression level."

Once at the Broad, take the elevators to the second floor, exiting left.  The event will be in the Monadnock room.  Please RSVP early and accurately so that we may better plan the event.  

BAGIM is sponsored by Scilligence, OpenEye Scientific Software, Schrodinger, Chemical Computing Group, ARIAD Pharmaceuticals, Vertex Pharmaceuticals, the Cambridge Crystallographic Data Centre, Optibrium, Dassault Systemes, Dotmatics, LabAnswer, and ChemAxon

Thursday, April 14, 2016

BAGIM Event: Dr. Tudor Oprea, May 11th starting at 6pm at the Harvard Faculty Club

Dr. Tudor Oprea of the University of New Mexico will present "Linking Drugs, Diseases, and the Druggable Proteome" at 6pm at the Harvard Faculty Club on Quincy Street in Cambridge, MA on May 11th. A social hour with refreshments will follow at John Harvard's Brewery and Ale House at 33 Dunster St. 

Please RSVP early and accurately to help us best plan for our event. 

BAGIM is sponsored by Scilligence, OpenEye Scientific Software, Schrodinger, Chemical Computing Group, ARIAD Pharmaceuticals, Vertex Pharmaceuticals, the Cambridge Crystallographic Data Centre, Optibrium, Dassault Systemes, Dotmatics, LabAnswer, and ChemAxon

Monday, March 28, 2016

BAGIM Event: Dr. Paul Clemons and Dr. Mathias Wawer, April 28th starting at 6pm at the Broad Institute

Dr. Paul Clemons and Dr. Mathias Wawer will present "Chemical diversity expressed through small-molecule performance: diverse readouts, phenotypes, and genetic determinants" on Thursday, April 28, 2016 at 7pm, following refreshments at 6pm, at the Broad Institute, 415 Main St. Cambridge MA. 

Once at the Broad, take the elevators to the second floor, exiting left. Food and drink will be in the Yellowstone room, and the presentation in the Monadnock room. Please RSVP  early and accurately so that we may better plan the event. 

BAGIM is sponsored by Scilligence, OpenEye Scientific Software, Schrodinger, Chemical Computing Group, ARIAD Pharmaceuticals, Vertex Pharmaceuticals, the Cambridge Crystallographic Data Centre, Optibrium, Dassault Systemes, Dotmatics, LabAnswer, and ChemAxon

Monday, February 22, 2016

Equinox Party and BAGIM Networking Event March 22nd, 2016

Come and celebrate the Spring Equinox with drinks and food at The Asgard Irish Pub & Restaurant Tuesday, March 22nd, from 5-7:30pm. The Asgard is at 350 Massachusetts Avenue, Cambridge, MA. This is a networking event for BAGIM members.
Please note that the guest list for this event is limited to 40 BAGIM members. RSVP here.  
We will add additional names on a waiting list after we receive 40 RSVPs. Please be accurate in your replies, and please if your plans change reverse your RSVP so that others can attend.
We're looking forward to seeing you there smile emoticon
BAGIM is sponsored by Scilligence, OpenEye Scientific Software, Schrodinger, Chemical Computing Group, ARIAD Pharmaceuticals, Vertex Pharmaceuticals, the Cambridge Crystallographic Data Centre, Optibrium, Dassault Systemes, Dotmatics, LabAnswer, and ChemAxon

Thursday, January 14, 2016

BAGIM Event: Dr. Penny Beuning at Vertex, Monday February 1st, starting at 6pm



Dr. Penny Beuning of Northeastern University will present "Specificity of Potentially Mutagenic DNA Polymerases for Different Types of DNA Damage" on Monday, February 1st at 7 pm following refreshments at 6 pm on the 9th floor of the Vertex One building on Northern Avenue. We are planning a larger, non-pizza meal which will include vegetarian options and drinks before the talk. 

Please see Dr. Beuning's research lab page

Please RSVP for this event

BAGIM is sponsored by Scilligence, OpenEye Scientific Software, Schrodinger, Chemical Computing Group, ARIAD Pharmaceuticals, Vertex Pharmaceuticals, the Cambridge Crystallographic Data Centre, Optibrium, Dassault Systemes, Dotmatics, LabAnswer, and ChemAxon