Biophysical experiments and biomolecular simulations: A perfect match?

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

New developments in force fields for biomolecular simulations

(2018) Paul S Nerenberg et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

(2018) Tristan Bereau et al.   JOURNAL OF CHEMICAL PHYSICS

Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)

(2018) João Marcelo Lamim Ribeiro et al.   JOURNAL OF CHEMICAL PHYSICS

An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations

(2018) Riccardo Capelli et al.   JOURNAL OF CHEMICAL PHYSICS

Frequency adaptive metadynamics for the calculation of rare-event kinetics

(2018) Yong Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics

(2018) Christoph Wehmeyer et al.   JOURNAL OF CHEMICAL PHYSICS

Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models

(2018) Purushottam D. Dixit et al.   Journal of Chemical Theory and Computation

Learning Effective Molecular Models from Experimental Observables

(2018) Justin Chen et al.   Journal of Chemical Theory and Computation

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multiplex assessment of protein variant abundance by massively parallel sequencing

(2018) Kenneth A. Matreyek et al.   NATURE GENETICS

RNA force field with accuracy comparable to state-of-the-art protein force fields

(2018) Dazhi Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Developing a molecular dynamics force field for both folded and disordered protein states

(2018) Paul Robustelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

(2018) Takanori Nakane et al.   eLife

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations

(2018) Sandro Bottaro et al.   Science Advances

Multiscale methods in drug design bridge chemical and biological complexity in the search for cures

(2018) Rommie E. Amaro et al.   Nature Reviews Chemistry

Extreme disorder in an ultrahigh-affinity protein complex

(2018) Alessandro Borgia et al.   NATURE

Metadynamic metainference: Convergence towards force field independent structural ensembles of a disordered peptide

(2017) Thomas Löhr et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

M3: an integrative framework for structure determination of molecular machines

(2017) Ezgi Karaca et al.   NATURE METHODS

Combining experimental and simulation data of molecular processes via augmented Markov models

(2017) Simon Olsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations

(2017) Sofie V. Nielsen et al.   PLoS Genetics

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan

(2016) Vytautas Gapsys et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Simple Method for Automated Equilibration Detection in Molecular Simulations

(2016) John D. Chodera   Journal of Chemical Theory and Computation

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

(2016) Karl T. Debiec et al.   Journal of Chemical Theory and Computation

Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation

(2016) Nicola Salvi et al.   Journal of Physical Chemistry Letters

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Metainference: A Bayesian inference method for heterogeneous systems

(2016) M. Bonomi et al.   Science Advances

Blind protein structure prediction using accelerated free-energy simulations

(2016) A. Perez et al.   Science Advances

Bayesian ensemble refinement by replica simulations and reweighting

(2015) Gerhard Hummer et al.   JOURNAL OF CHEMICAL PHYSICS

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

Integrative, dynamic structural biology at atomic resolution—it's about time

(2015) Henry van den Bedem et al.   NATURE METHODS

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

(2015) Christina Bergonzo et al.   RNA

Structural origin of slow diffusion in protein folding

(2015) H. S. Chung et al.   SCIENCE

The origins, determinants, and consequences of human mutations

(2015) J. Shendure et al.   SCIENCE

ENCORE: Software for Quantitative Ensemble Comparison

(2015) Matteo Tiberti et al.   PLoS Computational Biology

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Building Force Fields: An Automatic, Systematic, and Reproducible Approach

(2014) Lee-Ping Wang et al.   Journal of Physical Chemistry Letters

MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations

(2014) I. Ohmura et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts

(2014) W. Boomsma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combining Experiments and Simulations Using the Maximum Entropy Principle

(2014) Wouter Boomsma et al.   PLoS Computational Biology

The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics

(2013) Jason D. Tubbs et al.   BIOCHEMISTRY

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

(2012) Levi C.T. Pierce et al.   Journal of Chemical Theory and Computation

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Systematic Validation of Protein Force Fields against Experimental Data

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

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Crystal Structure and Allosteric Activation of Protein Kinase C βII

(2011) Thomas A. Leonard et al.   CELL

Transition path sampling of protein conformational changes

(2011) Jarek Juraszek et al.   CHEMICAL PHYSICS

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

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

The Energy Computation Paradox and ab initio Protein Folding

(2011) John C. Faver et al.   PLoS One

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Atomically detailed simulation of the recovery stroke in myosin by Milestoning

(2010) R. Elber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution

(2007) Matej Praprotnik et al.   Annual Review of Physical Chemistry

Experimental Parameterization of an Energy Function for the Simulation of Unfolded Proteins

(2007) Anders B. Norgaard et al.   BIOPHYSICAL JOURNAL