CS 371 ScheduleReadings and presentation slides are in the table below.

Please note: Students are expected to read the main papers before each class, but the additional papers are optional. Presenters and critiquers are expected to read both the main papers and additional papers listed for their topic.

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