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.

Saturday, March 16, 2024

BAGIM Happy Hour


Join us for a BAGIM happy hour sponsored by Discngine at Cambridge Brewing Company. Connect and network with other Boston based computational chemists, modelers and informaticians working in biotech and pharma!

Date/Time: April 18 from 6-8pm

Location: Cambridge Brewing Company

RSVP if you plan on attending so that we can get a headcount ahead of time.

Robert Parrish - High Performance Quantum Chemistry Methods for Pharmacology



We are hosting a joint BAGIM and QC Ware in-person event in May. We are welcoming Robert Parrish with the presentation High Performance Quantum Chemistry Methods for Pharmacology

Date: May 21, 2024 @ 6:00 PM

RSVP by May 16th. Registration will close on that day for this event.

Location: Batifol Cambridge ( 291 Third St, Cambridge, MA 02142 )

5:45 PM - Registration / Sign-in
6:00 PM - 7:00 PM - Presentation & Q&A
7:00 PM - 9:00 PM - Reception / Social Gathering with Food & Drink

Please arrive early to get checked in. We will hosting a social networking event after the presentation.  Event is capped at 60 participants

Hosts: BAGIM & QC Ware

Title: High Performance Quantum Chemistry Methods for Pharmacology

Speaker: Robert Parrish, SVP QC Ware and Quantum Chemist

Abstract: This talk details recent progress at QC Ware to make high-accuracy quantum chemical workflows fast, robust, and insightful enough for production use in mainline small-molecule ligand discovery programs. We discuss common molecular design workflows such as conformer search, torsion scan, intrinsic reaction coordinate optimization, and transition state optimization, as well as pharmacology-specific workflows for ligand-protein interaction analysis such as the functional group extension of symmetry adapted perturbation theory (F-SAPT). All of these methods are implemented in a brand new quantum chemistry engine specifically optimized for modern NVIDIA GPUs such as A100, and the resultant workflows are generally tractable on order of minutes for ~100 atom systems and on the order of hours for 1000+ atom systems, all with complete modern density functional theory methodology with large Gaussian basis sets possible. The complete toolset is available for general usage by computational or medicinal chemists in the "Promethium" SaaS environment.

Bio: Rob Parrish leads the quantum chemistry technology mission at QC Ware. Rob has spent the bulk of his early career learning how to use many types of hardware to accelerate quantum chemistry codes, including CPUs, GPUs, and even some forays into forthcoming QPUs. He has key interests in getting either more detailed or more complete information out of quantum chemistry codes, as exemplified by his efforts to robustly decompose interaction energies with "F-SAPT" methodology or to provide complete workflows for experimental observables like spectroscopies and conformer distributions. Rob operates under the strong hypothesis that quantum chemistry is imminently due to provide the same digital transformation to chemistry that computational fluid dynamics did for aeronautical engineering, and works daily to be a small part of that transformation.

Chris Williams - Autoph4: Pharmacophore Analysis of Multiple Protein Structures



We are hosting an April BAGIM in-person event with CCG. We welcome Chris Williams with the presentation Database autoph4: Pharmacophore Analysis of Multiple Protein Structures.

Date: April 24, 2024 @ 6:00 PM

LocationLe Meridien Boston Cambridge, 20 Sidney Street, Cambridge, MA, 02139 (MAP) - We will be in meeting room: Hunsaker Ballroom

6:00 PM - 6:45 PM - Presentation & Q&A
6:45 PM - onward - Reception

Please arrive early to get checked in. CCG is hosting free workshop on the same day (April 24). Please visit their website (HERE) for more information and to sign-up.

More information to be posted.

Host: Chemical Computing Group and BAGIM

Speaker: Chris Williams, PhD, Principal Scientist, Chemical Computing Group


An automated approach to summarize pocket shapes and binding hot-spots from a collection of protein structures is presented. Pocket shapes are described using pocket volumes derived from Alpha Sites and molecular surfaces. Binding hot-spots are located using pharmacophore features generated by AutoPH4. Collections of pocket volumes and pharmacophores are analyzed using feature densities which map onto a universal grid the fraction of structures that possess a given feature at each point in space. Regions with high pharmacophore feature densities identify the most persistent interaction binding hot-spots over the collection of structures. Pocket volume densities detect and classify binding site regions into core pockets and sub-pocket regions. Fingerprints that represent pocket shape, sub-pocket presence and pharmacophore feature presence are derived and used to cluster and classify multiple protein structures using standard fingerprint clustering tools. Application of the method to fragment-based drug design, minor pocket detection, selectivity mapping, binding-mode classification and custom docking scoring function creation is presented.