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.

Wednesday, January 25, 2017

BAGIM Event: Dr. Matthew Segall Wed March 1 at Millennium Takeda

Dr. Matthew Segall, CEO of Optibrium, will present "Predicting Routes, Sites and Products of Metabolism by Cytochrome P450 " on Wednesday March 1, starting at 6pm at the Millennium Takeda Oncology building at 35 Landsdowne St in Cambridge.  Refreshments and networking will follow at Asgard, 350 Massachusetts Ave in Cambridge.

Please RSVP to help us plan for this event.


In this presentation, we will describe recent developments to a method for predicting Cytochrome P450 (P450) metabolism that combines quantum mechanical (QM) simulations to estimate the reactivity of potential sites of metabolism on a compound with a ligand-based approach to account for the effects of orientation and steric constraints due to the binding pockets of different P450 isoforms (DOI: 10.1021/acs.jcim.6b00233). These new developments include modelling reaction pathways for epoxidation and developing models for an extended range of P450 isoforms. The resulting models achieve accuracies of 85-90% on independent test sets.

The metabolites resulting from oxidation at each potential site of metabolism can also be predicted, to guide experimental metabolite identification and highlight potentially active, reactive or toxic metabolites for further investigation. However, as the regioselectivity of metabolism may be different for each isoform, to predict the profile of metabolites that are likely to be formed, it is also necessary to identify which isoforms will be responsible for the metabolism of a compound. We will describe the latest results of our research to develop an accurate ‘WhichP450’ model, which can be coupled with isoform-specific regioselectivity models to generate a ranked list of expected metabolites.

Biography for Matthew Segall

Matt is CEO of Optibrium. He has a Master of Science in computation from the University of Oxford and a Ph.D. in theoretical physics from the University of Cambridge. As Associate Director at Camitro (UK), ArQule Inc. and then Inpharmatica, he led a team developing predictive ADME models and state-of-the-art intuitive decision-support and visualization tools for drug discovery. In January 2006, he became responsible for management of Inpharmatica's ADME business, including experimental ADME services and the StarDrop software platform. Following acquisition of Inpharmatica, Matt became Senior Director responsible for BioFocus DPI's ADMET division and in 2009 led a management buyout of the StarDrop business to found Optibrium, which develops software for small molecule design, optimisation and data analysis. Matt has published over 30 peer-reviewed papers and book chapters on computational chemistry, cheminformatics and drug discovery.

Thursday, January 19, 2017

BAGIM Event: Dr. John Conway & panel discussion on Cloud Computing Tuesday 2/7, at Vertex

Dr. John Conway of LabAnswer will present a lecture concerning cloud computing strategies for discovery research starting at 6pmon Tuesday, February 7th in the 9th floor multipurpose room of building 1 at Vertex Pharmaceuticals at 50 Northern Avenue, Boston. A panel discussion with Q/A on cloud computing will follow with Chris Waller from Merck, Dave Johnson from Moderna, and Steve Litster from Novartis. Networking will follow at approximately 7:30pm, more details TBD. 

Please RSVP  with your real first and last names to speed the sign in process at Vertex. You will find additional information there about the contents of the presentation.

Abstract: Many discovery research organizations struggle with their research informatics environments. Startups and new ventures may have these problems for reasons different than more established discovery research organizations. One observation for startups is the lack of resources or time to focus on strategic thinking and planning because researchers and supporting IT are consumed by tactical priorities and decisions. Defining criteria for decision making and future direction is imperative to a solid scientific data strategy and now with the cloud as an option; an infrastructure strategy. Newer organizations might choose a strict cloud environment where more established organizations will start to migrate towards cloud and will most likely result in a hybrid (on-premise/cloud) environment. From a scientific software vendor perspective, multi-tenant cloud solutions/platforms have the ability to solve and reduce many costly processes, interactions, and problems. From a client perspective, the cloud affords the opportunities of plug and play, reduced internal IT footprint, more efficient collaboration and faster adoption. This BAGIM event is to discuss and generate observations in the discovery research industry with respects to cloud informatics and computational approaches and solutions and to generate a report for the BAGIM community based on the resulting observations and discussions. Topics to be discussed include adoption, implementation, successes, failure, and the future.

BAGIM is sponsored by Dassault Systemes, DNASTAR, LabAnswer, Schrodinger, Silicon Therapeutics, Acellera, Acpharis, Cambridge Crystallographic Data Centre, Chemical Computing Group, Cresset, Cyrus Biotechnology, Dotmatics, Optibrium, Team Arrayo, and Scilligence

Friday, January 6, 2017

BAGIM Event: Dr. John Burke Thursday January 19 at The Broad Institute

Dr. John Burke, CEO of Applied BioMath, will present "Quantitative Modeling and Simulation Approaches: Driving Critical Decisions from Research through Clinical Trials" at the Broad Institute at 415 Main Street in Cambridge on Thursday, January 19th.  The talk will begin at 6pm in the auditorium and be followed by refreshments and networking at Meadhall at 4 Cambridge Center starting around 7pm.   Please RSVP for the meeting. 

Abstract: Quantitative Systems Pharmacology (QSP) is a mathematical modeling and engineering approach to translational medicine that aims to quantitatively integrate knowledge about therapeutics with an understanding of its mechanism of action in the context of human disease mechanisms. The goal of QSP modeling is “to understand, in a precise, predictive manner, how drugs modulate cellular networks in space and time and how they impact human pathophysiology [1].” In doing so, QSP approaches de-risk projects, accelerate the development of best in class therapeutics, and reduce late stage attrition rates. This results is helping industry save money, accelerate timelines, and make better therapeutics, ultimately improving patients’ lives. In the five years since the NIH QSP Working Group met last on this topic, progress has been made to advance this science and to integrate QSP approaches in the drug discovery and development process in industry. Here several case studies will be shown that highlights examples of QSP efforts that have accelerated the discovery and development of best-in-class therapeutics, and impacted critical decisions, in the continuum from preclinical exploration to clinical research. Examples include: providing biological understanding, impacts on new target proposals, lead generation, clinical candidate selection, IND support, and clinical trial go/no go decisions from industry.

1. Sorger, PK, et al. Quantitative and Systems Pharmacology in the Post-genomic Era: New Approaches to Discovering Drugs and Understanding Therapeutic Mechanisms. An NIH White Paper, QSP Workshop Group R. Ward, Editor. 2011.

Dr. Burke is CEO, President and Co-founder of Applied BioMath. He earned his PhD in Applied Mathematics from Arizona State University, completed a senior postdoctoral fellowship in Biological Engineering at Massachusetts Institute of Technology, and was Co-Scientific Director of the Cell Decision Process Center at Harvard Medical School, a NIH Center of Excellence. While at MIT and HMS he provided systems consulting support for large and small pharma and biotechs (e.g., AstraZeneca, Pfizer, Momenta), and software companies (e.g., Jacobian and MathWorks). Next he was at Merrimack Pharmaceuticals as a Senior Mathematical Biologist. He then was Global Head of Systems Biology and Pharmacology at Boehringer Ingelheim (BI). He was responsible for starting, implementing, scaling, and managing the worldwide strategy, portfolio, and efforts of BI’s systems initiatives. In a span of five years his group supported over 120 milestone transitions and major decisions from new target stage, lead generation, clinical candidate selection, through clinical trial support. Project indications and platforms included Oncology, Metabolic Disease, CNS, Cardiovascular, Respiratory, Infectious Disease, Inflammation and Immunology for large molecules, fixed dose combinations, ADC, and cell therapies. He is presently an Adjunct Professor at University of Massachusetts, Lowell, developing a QSP course at Harvard Medical School to be taught in the Spring of 2017, an industry advisor for the NIH/NCATS “Translational Center of Tissue Chip Technologies” and the DARPA - MIT Human on a Chip Grant, and an advisor to the Mathematics Department, University of Massachusetts, Lowell

BAGIM is sponsored by Dassault Systemes, DNASTAR, LabAnswer, Schrodinger, Silicon Therapeutics, Acellera, Acpharis, Cambridge Crystallographic Data Centre, Chemical Computing Group, Cresset, Cyrus Biotechnology, Dotmatics, Optibrium, and Scilligence,