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 by emailing them to cs371-win1516-staff@lists.stanford.edu. Critiques must be submitted before the paper is presented in class.
Date Topic Slides Main Papers Additional Papers Presenter(s) Critiquers
1/5/16 Introduction slides Ron Dror
1/7/16 Simulation of drug targets and simulation analysis slides 1. Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs
2. Identifying localized changes in large systems: Change-point detection for biomolecular simulations
Ron Dror
1/12/16 No Class
1/14/16 Using multiplayer online video games for structure prediction and design 1. Predicting protein structures with a multiplayer online game
2. RNA design rules from a massive open laboratory
a. Scientific rigor through videogames
b. Crystal structure of a monomeric retroviral protease solved by protein folding game players
Rhiju Das 2. Anthony Ma
1/19/16 Machine learning on molecular structures 1. High Precision Prediction of Functional Sites in Protein Structures
2. AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery
a. Improving Structure-Based Function Prediction Using Molecular Dynamics
b. Convolutional Networks on Graphs for Learning Molecular Fingerprints
c. Large-scale prediction and testing of drug activity on side-effect targets
d. The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation
Ray Zhuang 1. Connor Brinton
2. Raphael Townshend
1/21/16 Alchemical methods for computing binding affinities of drug candidates 1. Alchemical Free Energy Calculations: Ready for Prime Time?
2. Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field
Alchemical free energy methods for drug discovery: progress and challenges John Cherian 1. Cayla Miller
2. Yoon Kim
1/26/16 Modern protein design 1. De novo design of a transmembrane Zn2+-transporting four-helix bundle
2. Computational design of ligand-binding proteins with high affinity and selectivity
a. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences
b. Principles for designing ideal protein structures
Rishi Bedi
Kira Watkins
1. Stevan Jeknic
1. Tim Abbott
2. Kalli Kappel
2. Brian Do
1/28/16 Coevolution methods for predicting structure from large numbers of genetic sequences 1. Large scale determination of previously unsolved protein structures using evolutionary information
2. Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
a. Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
b. From residue coevolution to protein conformational ensembles and functional dynamics
c. Protein structure prediction from sequence variation
Cayla Miller
Yuan Xue
1. Rishi Bedi
1. Maheetha Bharadwaj
2. Yingzhou Li
2. Tim Abbott
2/2/16 New methods for solving tough crystal structures 1. Super-resolution biomolecular crystallography with low-resolution data
2. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals
a. Improving the Accuracy of Macromolecular Structure Refinement at 7Å Resolution
b. Structural biology: ‘seeing’ crystals the XFEL way
c. A grid-enabled web service for low-resolution crystal structure refinement
d. Deformable elastic network refinement for low-resolution macromolecular crystallography
Yoon Kim
Arjun Aditham
1. Kevin Larsen
1. Kira Watkins
2. Rishi Bedi
2. Yuan Xue
2/4/16 Markov state models for molecular dynamics simulations 1. Everything you wanted to know about Markov State Models but were afraid to ask
2. Markov state models of biomolecular conformational dynamics
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9 Kolade Adebowale
Anthony Ma
1. Shirin Sadri
2. Connor Brinton
2. Anjan Dwaraknath
2/9/16 RNA Secondary Structure Prediction & Design of Protein/Nucleic Acid Complexes 1. Computational design of co-assembling protein–DNA nanowires
2. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
High-throughput mutate-map-rescue evaluates SHAPE- directed RNA structure and uncovers excited states Kalli Kappel
Kevin Larsen
1. Ray Zhuang
1. Kolade Adebowale
2. Anthony Ma
2/11/16 Computational methods for single-particle electron microscopy 1. A Bayesian View on Cryo-EM Structure Determination
2. Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging
a. A Primer to Single-Particle Cryo-Electron Microscopy
b. Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps
c. Prevention of overfitting in cryo-EM structure determination
Yingzhou Li
Rolando Perez
1. Kevin Larsen
1. Richard Tang
2. Long-huei Chen
2. Kalli Kappel
2/16/16 Protein-protein interactions 1. Structure-based prediction of protein–protein interactions on a genome-wide scale
2. Interactome3d: adding structural details to protein networks
Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution Connor Brinton
Raphael Townshend
1. Yingzhou Li
1. Rolando Perez
2. Brian Do
2. Yoon Kim
2/18/16 Three-dimensional genome architecture 1. Three-dimensional genome architecture: players and mechanisms
2. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome Tim Abbott
Brian Do
1. Arjun Aditham
2. Kira Watkins
2. Kolade Adebowale
2/23/16 Michael Levitt
2/25/16 Three-dimensional genome architecture 1. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
2. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Adrian Sanborn 1. Maheetha Bharadwaj
2. Stevan Jeknic
2. Long-huei Chen
3/1/16 Compressed sensing for fluorescence microscopy 1. Faster STORM using compressed sensing
2. Compressive fluorescence microscopy for biological and hyperspectral imaging
Fast compressed sensing analysis for super- resolution imaging using L1-homotopy Anjan Dwaraknath
Richard Tang
1. Yuan Xue
1. Raphael Townshend
2. Arjun Aditham
3/3/16 Machine learning on microscopy images 1. Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules
2. Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning
Maheetha Bharadwaj
Shirin Sadri
1. John Cherian
1. Richard Tang
2. Anjan Dwaraknath
3/8/16 Cellular-level simulation 1. ReaDDy - A Software for Particle-Based Reaction- Diffusion Dynamics in Crowded Cellular Environments
2. Computational modeling of cellular signaling processes embedded into dynamic spatial contexts
a. Fast monte carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces
b. ReaDDyMM: Fast Interacting Particle Reaction-Diffusion Simulations Using Graphical Processing Units
Stevan Jeknic
Long-huei Chen
1. Shirin Sadri
1. Cayla Miller
2. Rolando Perez
3/10/16 No Class