CS 371 TopicsList of topics and readings are in the table below.

Topic Main Papers Additional Papers
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
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
1. Fast monte carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces
2. ReaDDyMM: Fast Interacting Particle Reaction-Diffusion Simulations Using Graphical Processing Units
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
1. Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
2. From residue coevolution to protein conformational ensembles and functional dynamics
3. Protein structure prediction from sequence variation
Compressed sensing for superresolution 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
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
1. A Primer to Single-Particle Cryo-Electron Microscopy
2. Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps
3. Prevention of overfitting in cryo-EM structure determination
Genome architecture 1. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
2. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Integrative modeling of molecular complexes 1. Determining the architectures of macromolecular assemblies
2. Conformational States of Macromolecular Assemblies Explored by Integrative Structure Calculation
1. Molecular architecture of the yeast Mediator complex
2. A strategy for dissecting the architectures of native macromolecular assemblies
3. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Learning force fields 1. Learn on the Fly: A Hybrid Classical and Quantum-Mechanical Molecular Dynamics Simulation
2. Gaussian Approximation Potentials: The Accuracy of Quantum Mechanics, without the Electrons
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
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
1. Improving Structure-Based Function Prediction Using Molecular Dynamics
2. Convolutional Networks on Graphs for Learning Molecular Fingerprints
3. Large-scale prediction and testing of drug activity on side-effect targets
4. The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation
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
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
1. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences
2. Principles for designing ideal protein structures
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
1. Improving the Accuracy of Macromolecular Structure Refinement at 7Å Resolution
2. Structural biology: ‘seeing’ crystals the XFEL way
3. A grid-enabled web service for low-resolution crystal structure refinement
4. Deformable elastic network refinement for low-resolution macromolecular crystallography
New superresolution imaging methods 1. Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution
2. Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics
Super-resolution fluorescence imaging with single molecules
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
Tracking the motion of single molecules 1. Correlation of Dual Colour Single Particle Trajectories for Improved Detection and Analysis of Interactions in Living Cells
2. Robust single-particle tracking in live-cell time-lapse sequences
Precisely and accurately localizing single emitters in fluorescence microscopy