标题
Biophysical experiments and biomolecular simulations: A perfect match?
作者
关键词
-
出版物
SCIENCE
Volume 361, Issue 6400, Pages 355-360
出版商
American Association for the Advancement of Science (AAAS)
发表日期
2018-07-27
DOI
10.1126/science.aat4010
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- 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
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search