Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

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