| 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
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Alchemical free energy methods for drug discovery: progress and challenges
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| 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
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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
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| 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
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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
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| Compressed sensing for superresolution fluorescence microscopy |
1. Faster STORM using compressed sensing
2. Compressive fluorescence microscopy for biological and hyperspectral imaging
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Fast compressed sensing analysis for super- resolution imaging using L1-homotopy
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| 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
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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
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| 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
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Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
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| Integrative modeling of molecular complexes |
1. Determining the architectures of macromolecular assemblies
2. Conformational States of Macromolecular Assemblies Explored by Integrative Structure Calculation
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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
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| 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
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| 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
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| 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
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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
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| 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
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Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
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| 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
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1. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences
2. Principles for designing ideal
protein structures
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| 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
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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
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| 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
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Super-resolution fluorescence imaging with single molecules
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| Protein-protein interactions |
1. Structure-based prediction of protein–protein interactions on a genome-wide scale
2. Interactome3d: adding structural details to protein networks
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Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution
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| 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
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Precisely and accurately localizing single emitters in fluorescence microscopy
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