Recruiting machine learning methods for molecular simulations of proteins

Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings

(2018) Jiangyan Feng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks

(2018) Yang Liu et al.   Cell Systems

Molecular dynamics simulations reveal the conformational dynamics ofArabidopsis thalianaBRI1 and BAK1 receptor-like kinases

(2017) Alexander S. Moffett et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Improving the accuracy of Møller-Plesset perturbation theory with neural networks

(2017) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables

(2017) Mohammad M. Sultan et al.   Journal of Chemical Theory and Computation

Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations

(2017) Albert C. Pan et al.   Journal of Chemical Theory and Computation

Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems

(2017) Mohammad M. Sultan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity

(2017) Shriyaa Mittal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How machine learning could help to improve climate forecasts

(2017) Nicola Jones   NATURE

Single-molecule analysis of ligand efficacy in β2AR–G-protein activation

(2017) G. Glenn Gregorio et al.   NATURE

Automating drug discovery

(2017) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes

(2017) Eliodoro Chiavazzo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activation mechanism of the G protein-coupled sweet receptor heterodimer with sweeteners and allosteric agonists

(2017) Soo-Kyung Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes

(2017) Steven M. Ryckbosch et al.   Nature Communications

Accelerating physical simulations of proteins by leveraging external knowledge

(2017) Alberto Perez et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter

(2017) Asghar M. Razavi et al.   Scientific Reports

Enhanced unbiased sampling of protein dynamics using evolutionary coupling information

(2017) Zahra Shamsi et al.   Scientific Reports

Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain

(2017) Mohammad M. Sultan et al.   Scientific Reports

Inhibitor Discovery for the Human GLUT1 from Homology Modeling and Virtual Screening

(2016) Peter Man-Un Ung et al.   ACS Chemical Biology

Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2

(2016) Christian R. Schwantes et al.   BIOPHYSICAL JOURNAL

Deep Mutational Scans as a Guide to Engineering High Affinity T Cell Receptor Interactions with Peptide-bound Major Histocompatibility Complex

(2016) Daniel T. Harris et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape

(2016) Mikolai Fajer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

(2016) Yinglong Miao et al.   MOLECULAR SIMULATION

Can artificial intelligence create the next wonder material?

(2016) Nicola Nosengo   NATURE

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

Auto-encoder based dimensionality reduction

(2016) Yasi Wang et al.   NEUROCOMPUTING

Transition path theory analysis of c-Src kinase activation

(2016) Yilin Meng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiensemble Markov models of molecular thermodynamics and kinetics

(2016) Hao Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spectral gap optimization of order parameters for sampling complex molecular systems

(2016) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational heterogeneity of the calmodulin binding interface

(2016) Diwakar Shukla et al.   Nature Communications

Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking

(2016) Sudipto Mukherjee et al.   Scientific Reports

Markov State Models Provide Insights into Dynamic Modulation of Protein Function

(2015) Diwakar Shukla et al.   ACCOUNTS OF CHEMICAL RESEARCH

Structural Insights into the Dynamic Process of β 2 -Adrenergic Receptor Signaling

(2015) Aashish Manglik et al.   CELL

Modeling Molecular Kinetics with tICA and the Kernel Trick

(2015) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs

(2015) Maxwell I. Zimmerman et al.   Journal of Chemical Theory and Computation

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

Simulating the Distance Distribution between Spin-Labels Attached to Proteins

(2015) Shahidul M. Islam et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Massively parallel single-amino-acid mutagenesis

(2015) Jacob O Kitzman et al.   NATURE METHODS

Protein structure determination by combining sparse NMR data with evolutionary couplings

(2015) Yuefeng Tang et al.   NATURE METHODS

Dissecting enzyme function with microfluidic-based deep mutational scanning

(2015) Philip A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerating molecular simulations of proteins using Bayesian inference on weak information

(2015) Alberto Perez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for nucleotide exchange in heterotrimeric G proteins

(2015) R. O. Dror et al.   SCIENCE

Gating Topology of the Proton-Coupled Oligopeptide Symporters

(2015) Philip W. Fowler et al.   STRUCTURE

Free energy landscape of activation in a signalling protein at atomic resolution

(2015) F. Pontiggia et al.   Nature Communications

A network of molecular switches controls the activation of the two-component response regulator NtrC

(2015) Dan K. Vanatta et al.   Nature Communications

Cloud computing approaches for prediction of ligand binding poses and pathways

(2015) Morgan Lawrenz et al.   Scientific Reports

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening

(2015) Claire Colas et al.   PLoS Computational Biology

Molecular Dynamics Simulation and Experimental Verification of the Interaction between Cyclin T1 and HIV-1 Tat Proteins

(2015) Kaori Asamitsu et al.   PLoS One

Complex Pathways in Folding of Protein G Explored by Simulation and Experiment

(2014) Lisa J. Lapidus et al.   BIOPHYSICAL JOURNAL

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Variational Approach to Molecular Kinetics

(2014) Feliks Nüske et al.   Journal of Chemical Theory and Computation

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics

(2014) Jordane Preto et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop

(2013) Yilin Meng et al.   JOURNAL OF MOLECULAR BIOLOGY

Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron–Electron Resonance Spectroscopy

(2013) Benoît Roux et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural Refinement from Restrained-Ensemble Simulations Based on EPR/DEER Data: Application to T4 Lysozyme

(2013) Shahidul M. Islam et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Ab Initio Quantum Chemistry for Protein Structures

(2012) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

(2011) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories

(2011) Thomas J. Lane et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ligand discovery from a dopamine D3 receptor homology model and crystal structure

(2011) Jens Carlsson et al.   Nature Chemical Biology

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Activation mechanism of the  2-adrenergic receptor

(2011) R. O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments

(2011) K. A. Beauchamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphoproteomics for the Masses

(2010) Paul A. Grimsrud et al.   ACS Chemical Biology

Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water

(2010) Jeetain Mittal et al.   BIOPHYSICAL JOURNAL

Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models

(2010) Gregory R. Bowman et al.   Journal of Chemical Theory and Computation

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Systematic determination of order parameters for chain dynamics using diffusion maps

(2010) A. L. Ferguson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

(2009) Hernán Stamati et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Kernel methods in machine learning

(2008) Thomas Hofmann et al.   ANNALS OF STATISTICS

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation