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Workshop
Machine Learning for Structural Biology
Raphael Townshend · Stephan Eismann · Ron Dror · Ellen Zhong · Namrata Anand · John Ingraham · Wouter Boomsma · Sergey Ovchinnikov · Roshan Rao · Roshan Rao · Per Greisen · Rachel Kolodny · Bonnie Berger

Sat Dec 12 08:00 AM -- 06:00 PM (PST) @ None
Event URL: http://mlsb.io »

Spurred on by recent advances in neural modeling and wet-lab methods, structural biology, the study of the three-dimensional (3D) atomic structure of proteins and other macromolecules, has emerged as an area of great promise for machine learning. The shape of macromolecules is intrinsically linked to their biological function (e.g., much like the shape of a bike is critical to its transportation purposes), and thus machine learning algorithms that can better predict and reason about these shapes promise to unlock new scientific discoveries in human health as well as increase our ability to design novel medicines.

Moreover, fundamental challenges in structural biology motivate the development of new learning systems that can more effectively capture physical inductive biases, respect natural symmetries, and generalize across atomic systems of varying sizes and granularities. Through the Machine Learning in Structural Biology workshop, we aim to include a diverse range of participants and spark a conversation on the required representations and learning algorithms for atomic systems, as well as dive deeply into how to integrate these with novel wet-lab capabilities.

Sat 8:00 a.m. - 8:10 a.m.
Opening Remarks (Talk) Video
Raphael Townshend, Namrata Anand
Sat 8:10 a.m. - 8:12 a.m.
Michael Levitt intro (Intro)
Raphael Townshend
Sat 8:12 a.m. - 8:50 a.m.
Keynote -- Michael Levitt (Talk) Video
Michael Levitt, Raphael Townshend, Namrata Anand
Sat 8:50 a.m. - 8:51 a.m.
Charlotte Deane Intro (Intro) Video
Raphael Townshend
Sat 8:51 a.m. - 9:10 a.m.
Invited Talk 1 -- Charlotte Deane (Talk) Video
Charlotte Deane, Raphael Townshend, Namrata Anand
Sat 9:10 a.m. - 9:11 a.m.
Frank Noe Intro (Intro) Video
Raphael Townshend
Sat 9:11 a.m. - 9:30 a.m.
Invited Talk 5 -- Frank Noe (Talk) Video
Frank Noe, Raphael Townshend, Namrata Anand
Sat 9:30 a.m. - 9:31 a.m.
Andrea Thorn Intro (Intro) Video
Raphael Townshend
Sat 9:31 a.m. - 9:50 a.m.
Invited Talk 2 -- Andrea Thorn (Talk) Video
Andrea Thorn, Raphael Townshend, Namrata Anand
Sat 9:50 a.m. - 10:20 a.m.
Break
Sat 10:20 a.m. - 10:22 a.m.
David Baker Intro (Intro) Video
Raphael Townshend
Sat 10:22 a.m. - 11:00 a.m.
Keynote -- David Baker (Talk) Video
David Baker, Raphael Townshend, Namrata Anand
Sat 11:00 a.m. - 12:00 p.m.
Morning Poster Session (Poster Session)
Raphael Townshend
Sat 12:00 p.m. - 12:01 p.m.
Video

3 min each

Raphael Townshend
Sat 12:01 p.m. - 12:11 p.m.
Contributed Talk 1 (Talk) Video
Raphael Townshend, Roshan Rao
Sat 12:11 p.m. - 12:21 p.m.
Contributed Talk 2 (Talk) Video
Raphael Townshend, Roshan Rao
Sat 12:21 p.m. - 12:31 p.m.
Contributed Talk 3 (Talk) Video
Raphael Townshend, Roshan Rao
Sat 12:30 p.m. - 2:00 p.m.
Lunch
Raphael Townshend
Sat 2:00 p.m. - 2:01 p.m.
Debora Marks intro (Intro) Video
Raphael Townshend
Sat 2:01 p.m. - 2:20 p.m.
Invited Talk 4 -- Debora Marks (Talk) Video
Debora Marks, Raphael Townshend, Namrata Anand
Sat 2:20 p.m. - 2:21 p.m.
Contributed talks intro (Intro) Video
Raphael Townshend
Sat 2:21 p.m. - 2:31 p.m.
Contributed Talk 4 (Talk) Video
Raphael Townshend, Namrata Anand
Sat 2:31 p.m. - 2:41 p.m.
Contributed Talk 5 (Talk) Video
Raphael Townshend, Namrata Anand
Sat 2:41 p.m. - 2:51 p.m.
Contributed Talk 6 (Talk) Video
Raphael Townshend, Namrata Anand
Sat 2:51 p.m. - 3:01 p.m.
Contributed Talk 7 (Talk) Video
Namrata Anand, Raphael Townshend
Sat 3:01 p.m. - 3:11 p.m.
Contributed Talk 8 (Talk) Video
Namrata Anand, Raphael Townshend
Sat 3:11 p.m. - 4:10 p.m.
Afternoon Poster Session (Poster Session)
Raphael Townshend
Sat 4:10 p.m. - 4:11 p.m.
Mohammed AlQuraishi intro (Intro) Video
Raphael Townshend
Sat 4:11 p.m. - 4:30 p.m.
Invited Talk 3 -- Mohammed AlQuraishi (Talk) Video
Mohammed AlQuraishi, Raphael Townshend, Namrata Anand
Sat 4:30 p.m. - 4:31 p.m.
Chaok Seok intro (Intro) Video
Raphael Townshend
Sat 4:31 p.m. - 4:50 p.m.
Invited Talk 6 -- Chaok Seok (Talk) Video
Chaok Seok, Raphael Townshend, Namrata Anand
Sat 4:50 p.m. - 5:00 p.m.
Concluding Remarks (Talk) Video
Raphael Townshend
Sat 5:00 p.m. - 6:00 p.m.
Happy Hour
Raphael Townshend
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GEFA: Early Fusion Approach in Drug-Target Affinity Prediction (Poster Session) [ Video ] Video
Roshan Rao
-
Designing a Prospective COVID-19 Therapeutic with Reinforcement Learning (Poster Session) [ Video ] Video
Roshan Rao
-
MXMNet: A Molecular Mechanics-Driven Neural Network Based on Multiplex Graph for Molecules (Poster Session) [ Video ] Video
Roshan Rao
-
Protein model quality assessment using rotation-equivariant, hierarchical neural networks (Poster Session) [ Video ] Video
Roshan Rao
-
Is Transfer Learning Necessary for Protein Landscape Prediction? (Poster Session) [ Video ] Video
Roshan Rao
-
Fast and adaptive protein structure representations for machine learning (Poster Session) [ Video ] Video
Roshan Rao
-
DHS-Crystallize: Deep-Hybrid-Sequence based method for predicting protein Crystallization (Poster Session) [ Video ] Video
Roshan Rao
-
Cross-Modality Protein Embedding for Compound-Protein Affinity and Contact Prediction (Poster Session) [ Video ] Video
Roshan Rao
-
Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models (Poster Session) [ Video ] Video
Roshan Rao
-
Profile Prediction: An Alignment-Based Pre-Training Task for Protein Sequence Models (Poster Session) [ Video ] Video
Roshan Rao
-
Exploring generative atomic models in cryo-EM reconstruction (Poster Session) [ Video ] Video
Roshan Rao
-
Pre-training Protein Language Models with Label-Agnostic Binding Pairs Enhances Performance in Downstream Tasks (Poster Session) [ Video ] Video
Roshan Rao
-
Sequence and stucture based deep learning models for the identification of peptide binding sites (Poster Session) [ Video ] Video
Roshan Rao
-
ESM-1b: Optimizing Evolutionary Scale Modeling (Poster Session) [ Video ] Video
Roshan Rao
-
Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization (Poster Session) [ Video ] Video
Roshan Rao
-
Conservative Objective Models: A Simple Approach to Effective Model-Based Optimization (Poster Session) [ Video ] Video
Roshan Rao
-
Learning Super-Resolution Electron Density Map of Proteins using 3D U-Net (Poster Session) [ Video ] Video
Roshan Rao
-
The structure-fitness landscape of pairwise relations in generative sequence models (Poster Session) [ Video ] Video
Roshan Rao
-
Combining variational autoencoder representations with structural descriptors improves prediction of docking scores (Poster Session) [ Video ] Video
Roshan Rao

Author Information

Raphael Townshend (Stanford University)
Stephan Eismann (Stanford University)
Ron Dror (Stanford)
Ellen Zhong (Massachusetts Institute of Technology)
Namrata Anand (Stanford University)
John Ingraham (Harvard University)
Wouter Boomsma (University of Copenhagen)
Sergey Ovchinnikov (Harvard)
Roshan Rao (UC Berkeley)
Roshan Rao (UC Berkeley)
Per Greisen (Novo Nordisk)
Rachel Kolodny (Haifa University)
Bonnie Berger (MIT)

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