Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins
出版年份 2022 全文链接
标题
Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins
作者
关键词
-
出版物
BIOCHEMICAL SOCIETY TRANSACTIONS
Volume -, Issue -, Pages -
出版商
Portland Press Ltd.
发表日期
2022-02-07
DOI
10.1042/bst20210499
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注意：仅列出部分参考文献，下载原文获取全部文献信息。- DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles
- (2021) Giulio Tesei et al. PLoS Computational Biology
- Machine Learning Force Fields
- (2021) Oliver T. Unke et al. CHEMICAL REVIEWS
- Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation
- (2021) Erik W Martin et al. NUCLEIC ACIDS RESEARCH
- Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins
- (2021) Jhullian J. Alston et al. METHODS
- Martini 3: a general purpose force field for coarse-grained molecular dynamics
- (2021) Paulo C. T. Souza et al. NATURE METHODS
- Improved coarse‐grained model for studying sequence dependent phase separation of disordered proteins
- (2021) Roshan Mammen Regy et al. PROTEIN SCIENCE
- FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices
- (2021) Eitan Lerner et al. eLife
- Resolving small distance variations by single-molecule FRET & EPR spectroscopy using rotamer libraries
- (2021) Daniel Klose et al. BIOPHYSICAL JOURNAL
- On the roles of intrinsically disordered proteins and regions in cell communication and signaling
- (2021) Sarah E. Bondos et al. Cell Communication and Signaling
- Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity
- (2021) Stéphanie Jephthah et al. Journal of Chemical Theory and Computation
- Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations
- (2021) Felix Kümmerer et al. Journal of Chemical Theory and Computation
- High Conformational Flexibility of the E2F1/DP1/DNA Complex
- (2021) Dana Saad et al. JOURNAL OF MOLECULAR BIOLOGY
- On the Potential of Machine Learning to Examine the Relationship Between Sequence, Structure, Dynamics and Function of Intrinsically Disordered Proteins
- (2021) Kresten Lindorff-Larsen et al. JOURNAL OF MOLECULAR BIOLOGY
- Highly accurate protein structure prediction with AlphaFold
- (2021) John Jumper et al. NATURE
- Highly accurate protein structure prediction for the human proteome
- (2021) Kathryn Tunyasuvunakool et al. NATURE
- Order and disorder—An integrative structure of the full-length human growth hormone receptor
- (2021) Noah Kassem et al. Science Advances
- Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data
- (2021) Francesco Pesce et al. BIOPHYSICAL JOURNAL
- Time-resolved X-ray scattering studies of proteins
- (2021) Hyun Sun Cho et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Empirical optimization of molecular simulation force fields by Bayesian inference
- (2021) Jürgen Köfinger et al. EUROPEAN PHYSICAL JOURNAL B
- Quantitative Description of Intrinsically Disordered Proteins Using Single-Molecule FRET, NMR, and SAXS
- (2021) Samuel Naudi-Fabra et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties
- (2021) Giulio Tesei et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions
- (2020) Jeong-Mo Choi et al. Annual Review of Biophysics
- Machine Learning for Molecular Simulation
- (2020) Frank Noé et al. Annual Review of Physical Chemistry
- Single-Molecule FRET of Intrinsically Disordered Proteins
- (2020) Lauren Ann Metskas et al. Annual Review of Physical Chemistry
- Biomolecular Phase Separation: From Molecular Driving Forces to Macroscopic Properties
- (2020) Gregory L. Dignon et al. Annual Review of Physical Chemistry
- Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution
- (2020) Andreas Haahr Larsen et al. PLoS Computational Biology
- Computational methods for exploring protein conformations
- (2020) Jane R. Allison BIOCHEMICAL SOCIETY TRANSACTIONS
- Glycine substitution in SH3-SH2 connector of Hck tyrosine kinase causes population shift from assembled to disassembled state
- (2020) Lei Huang et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems
- (2020) Paraskevi Gkeka et al. Journal of Chemical Theory and Computation
- Conformational Ensembles of an Intrinsically Disordered Protein Consistent with NMR, SAXS, and Single-Molecule FRET
- (2020) Gregory-Neal W. Gomes et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The dynamics of linear polyubiquitin
- (2020) Alexander Jussupow et al. Science Advances
- Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model
- (2020) Zakarya Benayad et al. Journal of Chemical Theory and Computation
- How do intrinsically disordered protein regions encode a driving force for liquid–liquid phase separation?
- (2020) Wade Borcherds et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Improvements to the ABSINTH forcefield for proteins based on experimentally derived amino-acid specific backbone conformational statistics
- (2019) Jeong-Mo Choi et al. Journal of Chemical Theory and Computation
- Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties
- (2019) Gül H. Zerze et al. Journal of Physical Chemistry Letters
- Commonly used FRET fluorophores promote collapse of an otherwise disordered protein
- (2019) Joshua A. Riback et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Simulating and analysing configurational landscapes of protein–protein contact formation
- (2019) Andrej Berg et al. Interface Focus
- SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures
- (2019) Gabor Nagy et al. Journal of Chemical Theory and Computation
- Molecular structure in biomolecular condensates
- (2019) Ivan Peran et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Enhancing NMR derived ensembles with kinetics on multiple timescales
- (2019) Colin A. Smith et al. JOURNAL OF BIOMOLECULAR NMR
- Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations
- (2019) Lisa M. Pietrek et al. Journal of Chemical Theory and Computation
- Membrane Anchoring of Hck Kinase via the Intrinsically Disordered SH4-U and Length Scale Associated with Subcellular Localization
- (2019) Matthew P. Pond et al. JOURNAL OF MOLECULAR BIOLOGY
- Temperature-Resolved Cryo-EM Uncovers Structural Bases of Temperature-Dependent Enzyme Functions
- (2019) Chin-Yu Chen et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy
- (2018) Massimiliano Bonomi et al. BIOPHYSICAL JOURNAL
- Interpreting solution X-ray scattering data using molecular simulations
- (2018) Jochen S Hub CURRENT OPINION IN STRUCTURAL BIOLOGY
- Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions
- (2018) Carolina Cragnell et al. JOURNAL OF MOLECULAR BIOLOGY
- Structural Ensemble Modulation upon Small-Molecule Binding to Disordered Proteins
- (2018) Gabriella T. Heller et al. JOURNAL OF MOLECULAR BIOLOGY
- On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations
- (2018) João Henriques et al. JOURNAL OF MOLECULAR BIOLOGY
- A Lattice Model of Charge-Pattern-Dependent Polyampholyte Phase Separation
- (2018) Suman Das et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Disordered peptide chains in an α-C-based coarse-grained model
- (2018) Łukasz Mioduszewski et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- 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
- Protein Phase Separation: A New Phase in Cell Biology
- (2018) Steven Boeynaems et al. TRENDS IN CELL BIOLOGY
- Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1
- (2018) Hamed Kooshapur et al. Nature Communications
- Sequence determinants of protein phase behavior from a coarse-grained model
- (2018) Gregory L. Dignon et al. PLoS Computational Biology
- AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins
- (2018) Hao Wu et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Precision DEER Distances from Spin-Label Ensemble Refinement
- (2018) Katrin Reichel et al. Journal of Physical Chemistry Letters
- Extreme disorder in an ultrahigh-affinity protein complex
- (2018) Alessandro Borgia et al. NATURE
- Molecular Dynamics Simulation for All
- (2018) Scott A. Hollingsworth et al. NEURON
- Biophysical experiments and biomolecular simulations: A perfect match?
- (2018) Sandro Bottaro et al. SCIENCE
- Determination of Structural Ensembles of Proteins: Restraining vs Reweighting
- (2018) Ramya Rangan et al. Journal of Chemical Theory and Computation
- The Antibody Light-Chain Linker Regulates Domain Orientation and Amyloidogenicity
- (2018) Benedikt Weber et al. JOURNAL OF MOLECULAR BIOLOGY
- Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers
- (2018) Andrej Berg et al. PLoS Computational Biology
- Determination of protein structural ensembles using cryo-electron microscopy
- (2018) Massimiliano Bonomi et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide
- (2017) Gabriella T. Heller et al. JOURNAL OF MOLECULAR BIOLOGY
- Biomolecular condensates: organizers of cellular biochemistry
- (2017) Salman F. Banani et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements
- (2017) Gustavo Fuertes et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles
- (2017) Sergei Grudinin et al. Acta Crystallographica Section D-Structural Biology
- Progress in small-angle scattering from biological solutions at high-brilliance synchrotrons
- (2017) Anne T. Tuukkanen et al. IUCrJ
- Coarse-Grained Protein Models and Their Applications
- (2016) Sebastian Kmiecik et al. CHEMICAL REVIEWS
- Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides
- (2016) Mike Reppert et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation
- (2016) Nicola Salvi et al. Journal of Physical Chemistry Letters
- Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods
- (2016) Alessandro Borgia et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- CHARMM36m: an improved force field for folded and intrinsically disordered proteins
- (2016) Jing Huang et al. NATURE METHODS
- Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS
- (2016) Mikayel Aznauryan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Coarse-grained modeling of the intrinsically disordered protein Histatin 5 in solution: Monte Carlo simulations in combination with SAXS
- (2016) Carolina Cragnell et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Metainference: A Bayesian inference method for heterogeneous systems
- (2016) M. Bonomi et al. Science Advances
- Structure-Free Validation of Residual Dipolar Coupling and Paramagnetic Relaxation Enhancement Measurements of Disordered Proteins
- (2015) Francisco N. Newby et al. BIOCHEMISTRY
- Bayesian ensemble refinement by replica simulations and reweighting
- (2015) Gerhard Hummer et al. JOURNAL OF CHEMICAL PHYSICS
- Analysis of Multidomain Protein Dynamics
- (2015) Amitava Roy et al. Journal of Chemical Theory and Computation
- Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment
- (2015) Sarah Rauscher et al. Journal of Chemical Theory and Computation
- Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment
- (2015) João Henriques et al. Journal of Chemical Theory and Computation
- Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
- (2015) Stefano Piana et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Intrinsically disordered proteins in cellular signalling and regulation
- (2015) Peter E. Wright et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Testing the transferability of a coarse-grained model to intrinsically disordered proteins
- (2015) Gil O. Rutter et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Targeting disordered proteins with small molecules using entropy
- (2015) Gabriella T. Heller et al. TRENDS IN BIOCHEMICAL SCIENCES
- Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States
- (2014) Ferruccio Palazzesi et al. Journal of Chemical Theory and Computation
- Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
- (2014) Robert B. Best et al. Journal of Chemical Theory and Computation
- Building Force Fields: An Automatic, Systematic, and Reproducible Approach
- (2014) Lee-Ping Wang et al. Journal of Physical Chemistry Letters
- 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
- Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments
- (2013) Dina Schneidman-Duhovny et al. BIOPHYSICAL JOURNAL
- Fast Real-Time NMR Methods for Characterizing Short-Lived Molecular States
- (2013) Enrico Rennella et al. CHEMPHYSCHEM
- Conformational Propensities of Intrinsically Disordered Proteins from NMR Chemical Shifts
- (2013) Jaka Kragelj et al. CHEMPHYSCHEM
- Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment
- (2013) Mike Reppert et al. JOURNAL OF CHEMICAL PHYSICS
- On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method
- (2013) Benoît Roux et al. JOURNAL OF CHEMICAL PHYSICS
- Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle
- (2013) Andrea Cavalli et al. JOURNAL OF CHEMICAL PHYSICS
- Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies
- (2013) Pilar Cossio et al. JOURNAL OF STRUCTURAL BIOLOGY
- An Introduction to Biological NMR Spectroscopy
- (2013) Dominique Marion MOLECULAR & CELLULAR PROTEOMICS
- Inference of Structure Ensembles of Flexible Biomolecules from Sparse, Averaged Data
- (2013) Simon Olsson et al. PLoS One
- The power of coarse graining in biomolecular simulations
- (2013) Helgi I. Ingólfsson et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables
- (2012) V. Ozenne et al. BIOINFORMATICS
- New developments in theATSASprogram package for small-angle scattering data analysis
- (2012) Maxim V. Petoukhov et al. JOURNAL OF APPLIED CRYSTALLOGRAPHY
- Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life
- (2012) Bin Xue et al. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
- On the Use of Experimental Observations to Bias Simulated Ensembles
- (2012) Jed W. Pitera 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
- A hierarchical algorithm for fast debye summation with applications to small angle scattering
- (2012) Nail A. Gumerov et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Mapping the Potential Energy Landscape of Intrinsically Disordered Proteins at Amino Acid Resolution
- (2012) Valéry Ozenne et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- A toolkit and benchmark study for FRET-restrained high-precision structural modeling
- (2012) Stanislav Kalinin et al. NATURE METHODS
- D2P2: database of disordered protein predictions
- (2012) Matt E. Oates et al. NUCLEIC ACIDS RESEARCH
- Systematic Validation of Protein Force Fields against Experimental Data
- (2012) Kresten Lindorff-Larsen et al. PLoS One
- SHIFTX2: significantly improved protein chemical shift prediction
- (2011) Beomsoo Han et al. JOURNAL OF BIOMOLECULAR NMR
- Accurate Distance Determination of Nucleic Acids via Förster Resonance Energy Transfer: Implications of Dye Linker Length and Rigidity
- (2011) Simon Sindbert et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering
- (2011) Pau Bernadó et al. Molecular BioSystems
- SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions
- (2011) Bartosz Różycki et al. STRUCTURE
- NMR-Based Protein Potentials
- (2010) Da-Wei Li et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Intrinsically disordered proteins are potential drug targets
- (2010) Steven J Metallo CURRENT OPINION IN CHEMICAL BIOLOGY
- Drugs for ‘protein clouds’: targeting intrinsically disordered transcription factors
- (2010) A Keith Dunker et al. CURRENT OPINION IN PHARMACOLOGY
- SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network
- (2010) Yang Shen et al. JOURNAL OF BIOMOLECULAR NMR
- NMR Characterization of Long-Range Order in Intrinsically Disordered Proteins
- (2010) Loïc Salmon et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy
- (2010) Niels Fischer et al. NATURE
- FoXS: a web server for rapid computation and fitting of SAXS profiles
- (2010) D. Schneidman-Duhovny et al. NUCLEIC ACIDS RESEARCH
- Rotamer libraries of spin labelled cysteines for protein studies
- (2010) Yevhen Polyhach et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Multidomain assembled states of Hck tyrosine kinase in solution
- (2010) S. Yang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Functional aspects of protein flexibility
- (2009) Kaare Teilum et al. CELLULAR AND MOLECULAR LIFE SCIENCES
- Theory, Practice, and Applications of Paramagnetic Relaxation Enhancement for the Characterization of Transient Low-Population States of Biological Macromolecules and Their Complexes
- (2009) G. Marius Clore et al. CHEMICAL REVIEWS
- Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances
- (2009) Kai J. Kohlhoff et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Detection of a Transient Intermediate in a Rapid Protein Folding Process by Solid-State Nuclear Magnetic Resonance
- (2009) Kan-Nian Hu et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The MARTINI Coarse-Grained Force Field: Extension to Proteins
- (2008) Luca Monticelli et al. Journal of Chemical Theory and Computation
- ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions
- (2008) Andreas Vitalis et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- NMR: prediction of molecular alignment from structure using the PALES software
- (2008) Markus Zweckstetter Nature Protocols
- Consistent blind protein structure generation from NMR chemical shift data
- (2008) Y. Shen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Experimental Parameterization of an Energy Function for the Simulation of Unfolded Proteins
- (2007) Anders B. Norgaard et al. BIOPHYSICAL JOURNAL
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