RM1 Symposium & EAC Meeting
Theme: protein-protein interactions, including antibodies
September 30 – October 1, 2021

Via Zoom. To register, please fill out this form.

Each session will have a 20 minute talk with 10 minutes for Q & A.
EAC (External Advisory Committee) meeting is at the end of the 2nd day.
All times Eastern

Thursday, September 30

12 pm – 12:05 Ken Dill, brief introductions and welcome
12:05 – 12:30 Barbara Hribar Lee, “Modelling aggregation of proteins in aqueous solutions”
12:30 – 1:00 Dima Kozakov, “Modeling and modulating protein interactions”
1:00 – 1:30 Gregory Dignon, “Computational Design of Excipient Formulations for Monoclonal Antibody Solutions”
1:30 – 2:00 break
2:00 – 2:30 Tom Truskett (EAC), “Modeling the interactions, solution structure, and viscosity of mAbs at high concentration”
2:30 – 3:00 Bernhardt Trout, “Machine Learning Techniques Applied to Developability: Aggregation and Viscosity”
3:00 – 3:30 Peter Tessier, “Measuring, predicting and optimizing antibody colloidal interactions”
3:30 – 4:00 Christopher Roberts, “Developability of Therapeutic Proteins from the Perspective of Electrostatic Protein-Protein Interactions”

Friday, October 1

12:00 – 12:30 Sandor Vajda (EAC), “Finding inhibitor binding sites in protein-protein interfaces”
12:30 – 1:00 Huan-Xiang Zhou, “Thermodynamic and Dynamic Properties of Phase-Separated Biomolecular Condensates”
1:00 – 1:30 Jeremy Schmit, “Physical Basis of Biomolecule Condensate Functionality”
1:30 – 2:00 break
2:00 – 2:30 Thomas Laue, “Protein-protein interactions in complex, concentrated solutions. Moving beyond molecular crowding”
2:30 – 3:00 Jayant Arora, “in silico models to predict protein viscosity and aggregation propensity to facilitate rapid drug product development”
3:00 – 3:15 Ken Dill, closing remarks
3:15 – 3:30 break
3:30 – 5:00 EAC meeting

RM1 PI’s:
Ken Dill, SBU
Vageli Coutsias, SBU
Chris Fennell, U OK
Barbara Hribar Lee, U Ljubljana, Slovenia
Dima Kozakov, SBU
Carlos Simmerling, SBU

Invited Speakers and participants
Jayant Arora, Regeneron
Gregory Dignon, SBU
Keith Johnston, UT Austin
Thomas Laue, New Hampshire
Christopher Roberts, Delaware
Jeremy Schmit, Kansas State
Peter Tessier, Michigan
Bernhardt Trout, MIT
Huan-Xiang Zhou, Chicago

External Advisory Committee (EAC):
David Case, Rutgers
Alex MacKerell, U Maryland
Valeria Molinero, U Utah
Tom Truskett, U Texas Austin
Sandor Vajda, Boston University

 

Public Zoom Talks

Upcoming Seminars:

  • October 7, 2021, 9 AM - 5 PM: SBU's Institute of Chemical Biology & Drug Discovery hosts the ICB&DD 15th Annual Symposium on, Covid-19/SARS-CoV-2 Antiviral Therapeutics Discovery.  The ICB&DD Annual Symposium is thematically focused on cutting-edge advances in chemical biology, structural and computational biology, cancer and infectious diseases, and drug discovery.  The Symposium invites renowned scholars in the field as well as highly recognized researchers on campus to present their exciting accomplishments and stimulate the exchange of innovative ideas among speakers, faculty, staff, and students on campus as well as researchers at the Brookhaven National Laboratory, academia and industries in the greater NY metropolitan area. 

The Plenary Lecturers this year are:  Dr. Sara Cherry, University of Pennsylvania; Dr. Rolf Hilgenfeld, University of Lübeck; Dr. Carolyn Machamer, Johns Hopkins University School of Medicine; Dr. Stanley Perlman, University of Iowa; Dr. Carlos Simmerling, Stony Brook University; Dr. David Veesler, University of Washington; Dr. Susan Weiss, University of Pennsylvania

Registration and/or Zoom details will be posted when available

Ongoing Seminars:

Past Seminars:

Laufer Center Researchers awarded Biomedical Sciences Innovation Funds from SBU


Laufer Center researchers, Markus Seeliger, Ivet Bahar, Robert Rizzo, and Iwao Ojima has been awarded Biomedical Sciences Innovation Funds from SBU.

This funding aims to integrate innovative structural biology techniques with computational biology and medicinal chemistry to develop drug lead compounds at a significantly faster rate than is currently possible. Thanks to the recent SBU-BNL seed award, we have established LI-XRA at SBU/BNL, a high-throughput workflow that allows for the determination of the structure of hundreds of proteins bound to target proteins. The purpose of this proposal is to analyze and interpret extensive amounts of data and predict the most promising combinations of fragments for drug development. Moreover, SBU-DD will offer the necessary infrastructure to test the binding of fragments identified in LI-XRA. LI-XRA is the only facility of its kind in the US and would be an invaluable resource for researchers in both academia and industry. This new initiative represents the next logical progression that capitalizes on SBU's expertise in computational biology at the Laufer Center. The collaboration between Stony Brook University and Brookhaven National Laboratories would synergize the advanced technologies in X-ray physics available at BNL with the computational and chemical expertise of scientists at SBU, paving the way to a large-scale collaborative research grant submission.

 

 

Sarah Gunasekera, a rising senior in the Honor College, is a double major in Applied Mathematics & Statistics and Biology, specializing in Quantitative Biology and Bioinformatics. She was recently awarded a Barry Goldwater Scholarship, and her independent research project under Dr. Carlos Simmerling involves using optimization methods to improve the computational tools used in RNA simulation. In her first year, Sarah began her undergraduate research journey with the Simmerling group, which led her to develop a profound appreciation for the ability of computational methods to enhance the efficiency and effectiveness of expensive and time-consuming wet-lab experiments. 
 
This summer, she will continue her RNA simulation project at Stony Brook University as a Frances Velay Fellow.
 

 

The URECA website regularly features students' perspectives on research and/or creative activities.
 
Sarah Gunasekera is a student in the Honors College double majoring in Applied Mathematics and Statistics, and Biology with a specialization in Quantitative Biology and Bioinformatics. Sarah was recently announced as a recipient of the 2023 Barry Goldwater Scholarship, a prestigious national award recognizing outstanding undergraduates in math, science, and engineering – one of two Stony Brook students to achieve this honor in 2023.
 
Under the mentorship of Dr. Carlos Simmerling (Dept. of Chemistry), she performs optimization experiments on small RNA structures to refine computational tools. Sarah is a co-author of a paper “Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir” published in the Journal of Chemical Theory and Computation; was awarded a URECA summer fellowship in 2022; and this summer will be continuing her work on RNA simulation tools as a Frances Velay Fellow.  
 
Sarah has presented at Chemistry Research Day (Fall 2022), and the URECA Symposium (Spring 2023); has served as a General Chemistry Teaching Assistant (Fall 2021); and has held leadership roles as Vice President (AY 21-22) and President (AY 23-24) of the Stony Brook Tennis Club.
 
 
For more of the interview, please go to: