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Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables

https://doi.org/10.1093/bioinformatics/bts172

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Machine-learning-based methods to generate conformational ensembles of disordered proteins

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Plasticity of an Ultrafast Interaction between Nucleoporins and Nuclear Transport Receptors

inferred← citeshttps://doi.org/10.1016/j.comptc.2026.115666openalex-snapshot

Decoding peptide structures and structural stability via conformational ensemble searching

inferred← citeshttps://doi.org/10.1016/j.csbj.2021.06.031openalex-snapshot

The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective

inferred← citeshttps://doi.org/10.1016/j.csbj.2021.09.009openalex-snapshot

Conformational landscape of multidomain SMAD proteins

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2026.154363openalex-snapshot

Bayesian reweighting of α-synuclein ensembles reveals local–global discrepancies between chemical shifts and chain dimensions

inferred← citeshttps://doi.org/10.1016/j.jbc.2025.108491openalex-snapshot

The ribonucleoprotein hnRNPA1 mediates binding to RNA and DNA telomeric G-quadruplexes through an RGG-rich region

inferred← citeshttps://doi.org/10.1016/j.jmb.2012.07.003openalex-snapshot

Ensemble Structure of the Modular and Flexible Full-Length Vesicular Stomatitis Virus Phosphoprotein

inferred← citeshttps://doi.org/10.1016/j.jmb.2013.10.031openalex-snapshot

Exploring the Minimally Frustrated Energy Landscape of Unfolded ACBP

inferred← citeshttps://doi.org/10.1016/j.jmb.2018.03.006openalex-snapshot

Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions

inferred← citeshttps://doi.org/10.1016/j.jmb.2018.03.007openalex-snapshot

An Extended Guinier Analysis for Intrinsically Disordered Proteins

inferred← citeshttps://doi.org/10.1016/j.jmb.2019.02.021openalex-snapshot

Dynamic Studies on Intrinsically Disordered Regions of Two Paralogous Transcription Factors Reveal Rigid Segments with Important Biological Functions

inferred← citeshttps://doi.org/10.1016/j.jmb.2020.03.014openalex-snapshot

Current approaches for integrating solution NMR spectroscopy and small-angle scattering to study the structure and dynamics of biomolecular complexes

inferred← citeshttps://doi.org/10.1016/j.jmb.2021.166899openalex-snapshot

Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR)

inferred← citeshttps://doi.org/10.1016/j.jmb.2023.168053openalex-snapshot

WASCO: A Wasserstein-based Statistical Tool to Compare Conformational Ensembles of Intrinsically Disordered Proteins

inferred← citeshttps://doi.org/10.1016/j.jmb.2025.169103openalex-snapshot

KDSAXS: A Tool for Analyzing Binding Equilibria With SAXS Data Using Explicit Models

inferred← citeshttps://doi.org/10.1016/j.jmb.2026.169862openalex-snapshot

Ensemblify: A User-friendly Platform for Generating and Analyzing Conformational Ensembles of Intrinsically Disordered Proteins and Regions

inferred← citeshttps://doi.org/10.1016/j.jmb.2026.170054openalex-snapshot

DC+: A web server for the analysis of residual dipolar couplings

inferred← citeshttps://doi.org/10.1016/j.jmgm.2019.01.009openalex-snapshot

Efficient construction of a diverse conformational library for amyloid-β as an intrinsically disordered protein

inferred← citeshttps://doi.org/10.1016/j.jmr.2013.11.011openalex-snapshot

NMR contributions to structural dynamics studies of intrinsically disordered proteins

inferred← citeshttps://doi.org/10.1016/j.jmr.2023.107539openalex-snapshot

Studies of proline conformational dynamics in IDPs by 13C-detected cross-correlated NMR relaxation

inferred← citeshttps://doi.org/10.1016/j.jsb.2020.107573openalex-snapshot

Structural ensemble and biological activity of DciA intrinsically disordered region

inferred← citeshttps://doi.org/10.1016/j.jsb.2022.107907openalex-snapshot

Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations

inferred← citeshttps://doi.org/10.1016/j.pnmrs.2014.08.001openalex-snapshot

NMR structure validation in relation to dynamics and structure determination

inferred← citeshttps://doi.org/10.1016/j.pnmrs.2018.07.001openalex-snapshot

Characterization of intrinsically disordered proteins and their dynamic complexes: From in vitro to cell-like environments

inferred← citeshttps://doi.org/10.1016/j.sbi.2013.02.007openalex-snapshot

Describing intrinsically disordered proteins at atomic resolution by NMR

inferred← citeshttps://doi.org/10.1016/j.sbi.2016.10.011openalex-snapshot

Small-angle scattering studies of intrinsically disordered proteins and their complexes

inferred← citeshttps://doi.org/10.1016/j.sbi.2023.102659openalex-snapshot

Nuclear magnetic resonance/single molecule fluorescence combinations to study dynamic protein systems

inferred← citeshttps://doi.org/10.1016/j.sbi.2023.102764openalex-snapshot

Overcoming challenges in structural biology with integrative approaches and nanobody-derived technologies

inferred← citeshttps://doi.org/10.1016/j.sbi.2025.103063openalex-snapshot

Biological insights from integrative modeling of intrinsically disordered protein systems

inferred← citeshttps://doi.org/10.1016/j.sbi.2025.103198openalex-snapshot

Advances in the determination of disordered protein ensemble

inferred← citeshttps://doi.org/10.1016/j.str.2013.10.020openalex-snapshot

Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and α-Synuclein in Solution from NMR and Small Angle Scattering

inferred← citeshttps://doi.org/10.1016/j.str.2014.01.003openalex-snapshot

Predicting the Predictive Power of IDP Ensembles

inferred← citeshttps://doi.org/10.1016/j.str.2014.03.012openalex-snapshot

Small-Angle X-Ray Scattering- and Nuclear Magnetic Resonance-Derived Conformational Ensemble of the Highly Flexible Antitoxin PaaA2

inferred← citeshttps://doi.org/10.1016/j.str.2015.03.009openalex-snapshot

The SH3 Domain Acts as a Scaffold for the N-Terminal Intrinsically Disordered Regions of c-Src

inferred← citeshttps://doi.org/10.1016/j.str.2015.06.002openalex-snapshot

Structural Impact of Tau Phosphorylation at Threonine 231

inferred← citeshttps://doi.org/10.1016/j.str.2017.02.011openalex-snapshot

The Unique Domain Forms a Fuzzy Intramolecular Complex in Src Family Kinases

inferred← citeshttps://doi.org/10.1016/j.str.2018.09.013openalex-snapshot

The Structure of the Pro-domain of Mouse proNGF in Contact with the NGF Domain

inferred← citeshttps://doi.org/10.1016/j.str.2018.10.016openalex-snapshot

Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database

inferred← citeshttps://doi.org/10.1016/j.str.2018.10.026openalex-snapshot

A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain

inferred← citeshttps://doi.org/10.1016/j.str.2019.05.001openalex-snapshot

Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression

inferred← citeshttps://doi.org/10.1016/j.str.2023.08.011openalex-snapshot

Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction

inferred← citeshttps://doi.org/10.1016/j.tibs.2012.08.006openalex-snapshot

Conditional disorder in chaperone action

inferred← citeshttps://doi.org/10.1016/j.virol.2018.08.012openalex-snapshot

Interplay between sequence, structure and linear motifs in the adenovirus E1A hub protein

inferred← citeshttps://doi.org/10.1016/j.ymeth.2018.04.006openalex-snapshot

Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics

inferred← citeshttps://doi.org/10.1017/s003358352300001xopenalex-snapshot

Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling

inferred← citeshttps://doi.org/10.1021/acs.biochem.7b00552openalex-snapshot

The LC8 Recognition Motif Preferentially Samples Polyproline II Structure in Its Free State

inferred← citeshttps://doi.org/10.1021/acs.chemrev.1c01023openalex-snapshot

NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins

inferred← citeshttps://doi.org/10.1021/acs.chemrev.5b00548openalex-snapshot

Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling

inferred← citeshttps://doi.org/10.1021/acs.chemrev.5b00562openalex-snapshot

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00807openalex-snapshot

Comprehensive Structural and Thermodynamic Analysis of Prefibrillar WT α‑Synuclein and Its G51D, E46K, and A53T Mutants by a Combination of Small-Angle X‑ray Scattering and Variational Bayesian Weighting

inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01196openalex-snapshot

Structural Insights into ATP-Sensitive Potassium Channel Mechanics: A Role of Intrinsically Disordered Regions

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00145openalex-snapshot

PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01107openalex-snapshot

Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00582openalex-snapshot

Are Protein Conformational Ensembles in Agreement with Experimental Data? A Geometrical Interpretation of the Problem

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00809openalex-snapshot

Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering

inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00370openalex-snapshot

Ensemble Docking for Intrinsically Disordered Proteins

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00928openalex-snapshot

Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00215openalex-snapshot

Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00259openalex-snapshot

Determination of Structural Ensembles of Flexible Molecules in Solution from NMR Data Undergoing Spin Diffusion

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00430openalex-snapshot

Accurate Calculation of Barnase and SNase Folding Energetics Using Short Molecular Dynamics Simulations and an Atomistic Model of the Unfolded Ensemble: Evaluation of Force Fields and Water Models

inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00014openalex-snapshot

Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method

inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00140openalex-snapshot

Simulations of the Upper Critical Solution Temperature Behavior of Poly(ornithine-co-citrulline)s Using MARTINI-Based Coarse-Grained Force Fields

inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00224openalex-snapshot

Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding

inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00971openalex-snapshot

Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation

inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00354openalex-snapshot

Generative Machine Learning of Conformational Ensembles of Intrinsically Disordered Proteins: Progress and Opportunities

inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00572openalex-snapshot

Experimentally Derived and Computationally Optimized Backbone Conformational Statistics for Blocked Amino Acids

inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00809openalex-snapshot

Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.1021/acs.jnatprod.2c00427openalex-snapshot

NMR-Based Configurational Assignments of Natural Products: How Floating Chirality Distance Geometry Calculations Simplify Gambling with 2N–1 Diastereomers

inferred← citeshttps://doi.org/10.1021/acs.jpca.2c03726openalex-snapshot

IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States

inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c02924openalex-snapshot

A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins

inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c05456openalex-snapshot

Incorporation of D2O-Induced Fluorine Chemical Shift Perturbations into Ensemble-Structure Characterization of the ERalpha Disordered Region

inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c04052openalex-snapshot

Delineating Structural Propensities of the 4E-BP2 Protein via Integrative Modeling and Clustering

inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c05701openalex-snapshot

Acetylation-Dependent Compaction of the Histone H4 Tail Ensemble

inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b04941openalex-snapshot

Thermodynamically–Weighted Conformational Ensemble of Cyclic RGD Peptidomimetics from NOE Data

inferred← citeshttps://doi.org/10.1021/acs.jpcb.6c02007openalex-snapshot

Filtering Disordered Protein Conformations by NMR Residual Dipolar Couplings

inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b05831openalex-snapshot

Molecular Determinants of Temperature Dependence of Protein Volume Change upon Unfolding

inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b05797openalex-snapshot

Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain

inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b07066openalex-snapshot

Atomistic Modeling of Intrinsically Disordered Proteins Under Polyethylene Glycol Crowding: Quantitative Comparison with Experimental Data and Implication of Protein–Crowder Attraction

inferred← citeshttps://doi.org/10.1021/acs.jpcb.9b07008openalex-snapshot

Molecular Dynamics with Orientational Tensorial Constraints: A New Approach to Probe the Torsional Angle Distributions of Small Rotationally Flexible Molecules

inferred← citeshttps://doi.org/10.1021/acs.jpclett.0c00288openalex-snapshot

Hydropathy Patterning Complements Charge Patterning to Describe Conformational Preferences of Disordered Proteins

inferred← citeshttps://doi.org/10.1021/acs.jpclett.4c00312openalex-snapshot

Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation

inferred← citeshttps://doi.org/10.1021/acs.jpclett.9b00850openalex-snapshot

Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties

inferred← citeshttps://doi.org/10.1021/acscentsci.7b00626openalex-snapshot

Looking at the Disordered Proteins through the Computational Microscope

inferred← citeshttps://doi.org/10.1021/acschembio.9b00679openalex-snapshot

Double Monoubiquitination Modifies the Molecular Recognition Properties of p15PAF Promoting Binding to the Reader Module of Dnmt1

inferred← citeshttps://doi.org/10.1021/acschemneuro.7b00446openalex-snapshot

From a Highly Disordered to a Metastable State: Uncovering Insights of α-Synuclein

inferred← citeshttps://doi.org/10.1021/acsomega.5c07620openalex-snapshot

pH Sensitivity of the SERF1a Conformational Ensemble

inferred← citeshttps://doi.org/10.1021/acsomega.8b00898openalex-snapshot

Conformational Ensembles Exhibit Extensive Molecular Recognition Features

inferred← citeshttps://doi.org/10.1021/cr4005082openalex-snapshot

Multisteric Regulation by Structural Disorder in Modular Signaling Proteins: An Extension of the Concept of Allostery

inferred← citeshttps://doi.org/10.1021/cr400514hopenalex-snapshot

Introducing Protein Intrinsic Disorder

inferred← citeshttps://doi.org/10.1021/cr4005692openalex-snapshot

Structural Disorder in Viral Proteins

inferred← citeshttps://doi.org/10.1021/cr400688uopenalex-snapshot

Exploring Free-Energy Landscapes of Intrinsically Disordered Proteins at Atomic Resolution Using NMR Spectroscopy

inferred← citeshttps://doi.org/10.1021/ja306905sopenalex-snapshot

Mapping the Potential Energy Landscape of Intrinsically Disordered Proteins at Amino Acid Resolution

inferred← citeshttps://doi.org/10.1021/ja4045532openalex-snapshot

Modulation of the Intrinsic Helix Propensity of an Intrinsically Disordered Protein Reveals Long-Range Helix–Helix Interactions

inferred← citeshttps://doi.org/10.1021/ja502030nopenalex-snapshot

Transient Electrostatic Interactions Dominate the Conformational Equilibrium Sampled by Multidomain Splicing Factor U2AF65: A Combined NMR and SAXS Study

inferred← citeshttps://doi.org/10.1021/ja511066qopenalex-snapshot

Visualizing the Molecular Recognition Trajectory of an Intrinsically Disordered Protein Using Multinuclear Relaxation Dispersion NMR

inferred← citeshttps://doi.org/10.1021/jacs.1c06264openalex-snapshot

Quantitative Description of Intrinsically Disordered Proteins Using Single-Molecule FRET, NMR, and SAXS

inferred← citeshttps://doi.org/10.1021/jacs.3c06965openalex-snapshot

Multivalent Dynamic Colocalization of Avian Influenza Polymerase and Nucleoprotein by Intrinsically Disordered ANP32A Reveals the Molecular Basis of Human Adaptation

inferred← citeshttps://doi.org/10.1021/jacs.3c10847openalex-snapshot

Quantitative Ensemble Interpretation of Membrane Paramagnetic Relaxation Enhancement (mPRE) for Studying Membrane-Associated Intrinsically Disordered Proteins

inferred← citeshttps://doi.org/10.1021/jacs.4c15653openalex-snapshot

Structural Context Modulates the Conformational Ensemble of the Intrinsically Disordered Amino Terminus of α-Synuclein

inferred← citeshttps://doi.org/10.1021/jacs.5b06027openalex-snapshot

Ensemble Methods Enable a New Definition for the Solution to Gas-Phase Transfer of Intrinsically Disordered Proteins

inferred← citeshttps://doi.org/10.1021/jacs.5b07765openalex-snapshot

Large-Scale Conformational Dynamics Control H5N1 Influenza Polymerase PB2 Binding to Importin α

inferred← citeshttps://doi.org/10.1021/jacs.6b06543openalex-snapshot

Finding Our Way in the Dark Proteome

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