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
1/9/17 Introduction slides Ron Dror
1/11/17 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
1/16/17 Guest talk: Virtual reality for structural biology (Optional) Eli Groban (Autodesk)
1/18/17 Using multiplayer online video games for structure prediction and design intro
1. Predicting protein structures with a multiplayer online game
2. RNA design rules from a massive open laboratory
3. Principles for predicting RNA Secondary Structure Design Difficulty
a. Scientific rigor through videogames
b. Crystal structure of a monomeric retroviral protease solved by protein folding game players
c. Algorithm discovery by protein folding game players
Seth Hildick-Smith
Jesse Min
Meera Srinivasan
1. Lawrence Murata
1. Julia Wang
2. Philip Scott DiGiacomo
2. Pavitra Rengarajan
3. Anika Naidu
1/23/17 Coevolution methods for predicting structure from large numbers of genetic sequences intro
1. Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
2. Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
3. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
a. Large scale determination of previously unsolved protein structures using evolutionary information
b. From residue coevolution to protein conformational ensembles and functional dynamics
c. Protein structure prediction from sequence variation
Jason Wang
Kaitlyn Lagattuta
Phillip DiGiacomo
1. Anika Naidu
1. Ambika Acharya
2. Seth Smith
3. Mila Shultz
3. Adithya Ganesh
1/25/17 Modern protein design intro
1. De novo design of a transmembrane Zn2+-transporting four-helix bundle
2. Accurate design of megadalton-scale two-component icosahedral protein complexes
3. Accurate de novo design of hyperstable constrained peptides
a. Computational design of ligand-binding proteins with high affinity and selectivity
b. Principles for designing ideal protein structures
Anika Naidu
Kevin Goncalves
Mila Shultz
1. Karen Lee
1. Julia Wang
2. Heejo Choi
2. Ambika Acharya
3. Will Hang
1/30/17 Machine learning for structured-based virtual screening intro
1. AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery
2. Learning Deep Architectures for Interaction Prediction in Structure-based Virtual Screening
3. Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening
a. Convolutional Networks on Graphs for Learning Molecular Fingerprints
b. A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking.
c. Boosting Docking-based Virtual Screening with Deep Learning
Victor Storchan
Christopher Vo
Lawrence Murata
1. Jason Wang
1. Daniel Fernandes
2. Mila Shultz
2. Alex Sly
3. Kaitlyn Lagattuta
3. Anika Nagpal
2/1/17 Improving virtual screening through physics-based methods intro
1. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery
Alchemical free energy methods for drug discovery: progress and challenges
3. 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
a. Alchemical Free Energy Calculations: Ready for Prime Time?
Wisam Reid
Miguel Camacho-Horvitz
Karen Lee
1. Axel Sly
1. Seth Hildick-Smith
2. Hugo Kitano
2. Pavitra Rengarajan
3. Kaitlyn Anne Lagattuta
3. Will Hang
2/6/17 New methods for solving tough crystal structures intro
1. Super-resolution biomolecular crystallography with low-resolution data
2. Guiding Belief Propagation using Domain Knowledge for Protein-Structure Determination
a. Assessing and maximizing data quality in macromolecular crystallography
b. A grid-enabled web service for low-resolution crystal structure refinement
c. Deformable elastic network refinement for low-resolution macromolecular crystallography
d. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals
e. Improving the Accuracy of Macromolecular Structure Refinement at 7Å Resolution
f. Linking Crystallographic Model and Data Quality
g. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
Daniel Byrnes
Hari Ravichandran
1. Masood Malekghassemi
1. Meera Srinivasan
1. Daniel Hogan
2. Jesse Min
2. Jenifer Brown
2/8/17 Markov state models for molecular dynamics simulations intro
1. Everything you wanted to know about Markov State Models but were afraid to ask
2. Markov state models of biomolecular conformational dynamics
3. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery
a. Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
b. Markov State Models Provide Insights into Dynamic Modulation of Protein Function
Michael Maduabum
Adithya Ganesh
Axel Sly
1. Daniel Byrnes
1. Miguel Camacho-Horvitz
2. Hugo Kitano
2. Phillip DiGiacomo
3. Victor Storchan
3. Christopher Vo
2/13/17 RNA Structure Prediction & Design of Protein/Nucleic Acid Complexes intro
1. Computational design of co-assembling protein–DNA nanowires
2. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
a. 3D RNA and Functional Interactions from Evolutionary Couplings
Julia Wang
Ambika Acharya
1. Alex Yoshikawa
1. Heejo Choi
1. Jason Wang
2. Meera Srinivasan
2. Michael Maduabum
2/15/17 Computational methods for single-particle electron microscopy intro
1. A Bayesian View on Cryo-EM Structure Determination
2.Trajectories of the ribosome as a Brownian machine
a. Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging
b. A Primer to Single-Particle Cryo-Electron Microscopy
c. Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps
d. Prevention of overfitting in cryo-EM structure determination
e.Molecular dynamics-based refinement and validation for sub-5 A? cryo-electron microscopy maps
f.Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics Simulation
Hugo Kitano
Daniel Hogan
1. Hari Ravichandran
1. Jesse Min
1. Jasmine Johnson
2. Daniel Byrnes
2. Leo Keselman
2. Wisam Reid
2/20/17 No Class
2/22/17 Protein-protein interactions intro
1. Structure-based prediction of protein–protein interactions on a genome-wide scale
2. Panorama of ancient metazoan macromolecular complexes
a.Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution
b. Interactome3d: adding structural details to protein networks
Anika Nagpal
Masood Malekghassemi
1. Christine Yiwen Yeh
1. Jenifer Brown
1. Raj Raina
2. Hari Ravichandran
2. Kevin Goncalves
2/27/17 Integrative modeling of molecular complexes intro
1. Determining the architectures of macromolecular assemblies
Conformational States of Macromolecular Assemblies Explored by Integrative Structure Calculation
Molecular architecture of the yeast Mediator complex
a. A strategy for dissecting the architectures of native macromolecular assemblies
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Christine Yiwen Yeh
Delaney Sullivan
Jenifer Brown
1. Alex Yoshikawa
1. Kevin Goncalves
2. Jenifer Brown
2. Masood Malekghassemi
3. Daniel Fernandes
3. Raj Raina
3/1/17 Three-dimensional genome architecture intro
1. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
2. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
a. Three-dimensional genome architecture: players and mechanisms
b. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
c. Comprehensive mapping of long-range interactions reveals folding principles of the human genome
Brad Krajina
Alex Yoshikawa
1. Anika Nagpal
1. Delaney Sullivan
2. Delaney Sullivan
2. Christine Yiwen Yeh
3/6/17 Machine learning on microscopy images intro
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
3. Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data
Ramin Ahmari
Will Hang
Pavitra Rengarajan
1. Leo Keselman
1. Christopher Vo
2. Brad Krajina
2. Miguel Camacho-Horvitz
3. Victor Storchan
3/8/17 Cellular-level simulation intro
1. ReaDDy - A Software for Particle-Based Reaction- Diffusion Dynamics in Crowded Cellular Environments
2. Decoding Information in Cell Shape
3. 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
Heejo Choi
Jasmine Johnson
Raj Raina
1. Michael Maduabum
1. Daniel Fernandes
2. Karen Lee
2. Ramin Ahmari
3. Wisam Reid
3/13/17 Superresolution fluorescence microscopy intro
1. Faster STORM using compressed sensing
2. Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution
a. Super-Resolution Fluorescence Imaging with Single Molecules
b. Robust single-particle tracking in live-cell time-lapse sequences
Leonid Keselman
Daniel Fernandes
1. Lawrence Lin Murata
1. Daniel Hogan
2. Ramin Ahmari
2. Brad Krajina
2. Jasmine Johnson
3/15/17 TBD