1/9/18 |
Introduction |
slides |
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Survey (due 1/12) |
Ron Dror |
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1/11/18 |
Guest Talk: Designing beyond rule-of-five molecules for tough targets |
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Alan Cheng |
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1/16/18 |
Simulation of drug targets and simulation analysis |
slides
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Ron Dror |
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1/18/18 |
Using multiplayer online video games for structure prediction and design |
intro
slides
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1. Thomas Choi
1. Tara Iyer
2. Jennifer Pulido
2. Xinyi Jiang
3. Trevor Tsue
3. Nikhil Goel
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1/23/18 |
Coevolution methods for predicting structure from large numbers of genetic sequences |
intro
slides
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- Alex Chu
- Samir Sen
- Ankit Baghel
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1. Nicholas Allen
2. Grady Day
2. Dev Bhargava
3. Eric Zhao
3. Daniel Hsu
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1/25/18 |
Modern protein design |
intro
slides
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- Jeffrey Chang
- Joyce Kang
- Sunwoo Kang
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1. Jenny Vo-Phamhi
1. Ramya Rangan
2. Niki Goularte
2. Grady Day
3. Anastasiya Vitko
3. Thomas Choi
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1/30/18 |
Improving
virtual screening
through
physics-based methods |
intro
slides
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1. Jeffrey Chang
1. Lydia Hamburg
2. Huanghao Mai
2. Rifath Rashid
3. Nithin Kannan
3. Veena Agusala
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2/1/18 |
Machine
learning for
structured-based
virtual screening |
intro
slides
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- Nithin Kannan
- Eric Zhao
- Daniel Hsu
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1. Robbie Ostrow
1. Nicholas Allen
2. Anvita Gupta
2. Shalom Rottman-Yang
3. Geoffrey Angus
3. Rooz Mahdavian
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2/6/18 |
Learning molecular energy functions |
intro
slides
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- Lydia Hamburg
- Anvita Gupta
- Evan Eyuboglu
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1. Noor Siddiqui
1. Alex Chu
2. Samir Sen
2. Trevor Tsue
3. Jimmy Yu
3. Jeffrey Chang
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2/8/18 |
Discovering cryptic binding sites |
intro
slides |
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- Ramya Rangan
- Anni Zhang
- Thomas Choi
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1. Lydia Hamburg
1. Peter Wang
2. Joyce Kang
2. Anvita Gupta
3. Ankit Baghel
3. Sunwoo Kang
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2/13/18 |
Protein-protein interactions |
intro
slides
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- Peter Wang
- Pallavi Krishnarao
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1. Sunwoo Kang
1. Noor Siddiqui
2. Paulina Chamely
2. Tymor Hamamsy
3. Huanghao Mai
3. Anastasiya Vitko
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2/15/18 |
Structure prediction/design for nucleic acids and complexes |
intro
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- Xinyi Jiang
- Tymor Hamamsy
- Nicholas Allen
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1. Yunha Hwang
1. Sarah Hull
2. Pallavi Krishnarao
2. Paulina Chamely
3. Evan Eyuboglu
3. Geoffrey Angus
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2/20/18 |
Guest Lecture: Scott Hollingsworth |
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Scott Hollingsworth
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2/22/18 |
Computational methods for single-particle cryo-electron microscopy |
intro
slides
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- Robbie Ostrow
- Trevor Tsue
- Shalom Rottman-Yang
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1. Ramya Rangan
1. Dhaval Gajiwala
2. Mika Jain
2. Samir Sen
3. Nikhil Goel
3. Veena Agusala
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2/27/18 |
Integrative modeling of molecular complexes |
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- Rifath Rashid
- Jenny Vo-Phamhi
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1. Jimmy Yu
1. Sarah Hull
2. Niki Goularte
2. Nithin Kannan
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3/1/18 |
Three-dimensional genome architecture |
intro
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- Sarah Hull
- Grady Day
- Paulina Chamely
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1. Jen Pulido
1. Yunha Hwang
2. Tymor Hamamsy
2. Joyce Kang
3. Sarang Nath
3. Pallavi Krishanrao
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3/6/18 |
Superresolution fluorescence microscopy |
intro
|
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Super-Resolution Fluorescence Imaging with Single Molecules
Robust single-particle tracking in live-cell time-lapse sequences
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- Yunha Hwang
- Niki Goularte
- Sarang Nath
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1. Robbie Ostrow
1. Dhaval Gajiwala
2. Shalom Rottman-Yang
2. Eric Zhao
3. Jenny Vo-Phamhi
3. Mika Jain
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3/8/18 |
Machine learning on microscopy images |
intro
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- Anastasiya Vitko
- Geoffrey Angus
- Mika Jain
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1. Xinyi Jiang
1. Anni Zhang
2. Daniel Hsu
2. Rifath Rashid
3. Rooz Mahdavian
3. Evan Eyuboglu
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3/13/18 |
Cellular-level simulation |
intro
class wrap-up
|
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- Jen Pulido
- Dhaval Gajiwala
- Veena Agusala
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1. Alex Chu
2. Peter Wang
2. Sarang Nath
3. Anni Zhang
3. Ankit Baghel
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3/15/18 |
Guest Talk: Jeff Blaney (Genentech): What have we learned in the 40 years since structure-based design began? |
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Jeff Blaney
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