Enabling Protein Structure Prediction with Artificial Intelligence at Rutgers and Beyond

Overview

On December 9, 2021, the Institute of Quantitative Biology (IQB) in collaboration with the Office of Advanced Research Computing (OARC) and the Office for Research offers a crash course on "Enabling Protein Structure Prediction with Artificial Intelligence at Rutgers and Beyond". This crash course will present a broad overview of how Artificial Intelligence/Machine Learning (AI/ML) methods are being used for de novo protein structure prediction and hands-on experience with the state-of-the-art AI methods - AlphaFold2 and RoseTTAFold. Both of these methods were based on deep neural networks and made revolutionary advancement in predicting the protein structures.

Agenda

1:00 - 1:05 P.M. Introductions
Stephen K. Burley, M.D., D.Phil.: Founding Director, Institute for Quantitative Biomedicine
J. Barr von Oehsen, Ph.D.: Associate Vice President, Office of Advanced Research Computing

1:05 - 1:10 P.M. Welcome and Crash Course Learning Objectives
Michael E. Zwick, Ph.D.: Senior Vice President, Office for Research

1:10 - 1:40 P.M. De Novo Protein Structure Prediction: Disruptive Transformation of Biology in 3D
Minkyung Baek, Ph.D.: University of Washington

1:40 - 2:10 P.M. Primer on Artificial Intelligence: Statistical Underpinning and Vocabulary
Sijian Wang, Ph.D.: IQB; SAS-Statistics

2:10 - 2:30 P.M. Potential for Impact on Research in Cell/Molecular, Cancer, and Structural Biology
Stephen K. Burley, M.D., D.Phil.: RCSB PDB; IQB; SAS-CCB; CINJ

Lightning Talks:

2:30 - 2:45 P.M. Experience with Applications in Single-particle Cryo-Electron Microscopy
Vasileios Petrou, Ph.D.: CII; RNJMS-MB&MG

2:45 - 3:00 P.M. Experience with Applications in Computational Biology
Guillaume Lamoureux, Ph.D.: CCIB; CCAS-Chemistry

3:00 - 3:15 P.M. Experience with Applications in SARS-CoV-2 Protease Modeling and Drug Discovery
Sagar Khare, Ph.D.: IQB; SAS-CCB; CINJ

3:15 - 3:30 P.M. Break

3:30 - 3:45 P.M. Primer: Getting Access to Rutgers Infrastructure (Amarel, AlphaFold2, RoseTTAFold)
Balamurugan Desinghu, Ph.D.: OARC

3:45 - 4:55 P.M. Hands On De Novo Protein Structure Prediction Tutorial

• Modeling/visualizing a small globular protein structure in real time
• Downloading pre-computed structure models from AlphaFoldDB
• Modeling your favorite protein using AlphaFold2 and RoseTTAFold (requires FASTA sequence or UniProt ID)

Balamurugan Desinghu, Ph.D., Paul Arias, Ph.D., Vlad Kholodovych Ph.D.,
Ehud Zelzion, Ph.D., Janet Chang, Ph.D.: OARC
Stephen K. Burley, M.D., D.Phil., Sagar Khare, Ph.D., Joseph Lubin, B.Sc.: IQB

5:00 P.M. Closing Remarks and Acknowledgements
Balamurugan Desinghu, Ph.D.: Senior Scientist, Office of Advanced Research Computing