ReviewBiomolecules2019
Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins.
Review in Biomolecules, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
35 citing papers in PubMed, 67 citations in OpenAlex.
- Amyloid-β, Tau Protein, α-Synuclein, TDP-43, and FUS in Mixed Pathology: And Intrinsic Disorder to Rule Them All.International journal of molecular sciences · 2026Review
- QuPepFold: A python package for hybrid quantum-classical protein folding simulations with CVaR-optimized VQE.PloS one · 2026Article
- Using Multiple Isotope-Labeled Infrared Spectra for the Structural Characterization of an Intrinsically Disordered Peptide.The journal of physical chemistry. B · 2025Article
- Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs.Frontiers in molecular biosciences · 2025Review
- Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences.Proteins · 2024Article
- CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules.JACS Au · 2024Article
- Biomolecular dynamics in the 21st century.Biochimica et biophysica acta. General subjects · 2024Review
- Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein.The Journal of chemical physics · 2023Article
- Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models.Journal of chemical information and modeling · 2023Article
- Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling.Quarterly reviews of biophysics · 2023Review
- Emerging Pharmacotherapeutic Strategies to Overcome Undruggable Proteins in Cancer.International journal of biological sciences · 2023Review
- Targeting disordered-structured domain interactions in Galectin-3 based on NMR and enhanced MD.Biophysical journal · 2022Article
- Combining enhanced sampling and deep learning dimensionality reduction for the study of the heat shock protein B8 and its pathological mutant K141E.RSC advances · 2022Article
- IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States.The journal of physical chemistry. A · 2022Article
- Optimizing Epitope Conformational Ensembles Using α-Synuclein Cyclic Peptide "Glycindel" Scaffolds: A Customized Immunogen Method for Generating Oligomer-Selective Antibodies for Parkinson's Disease.ACS chemical neuroscience · 2022Article
- Recognition of the TDP-43 nuclear localization signal by importin α1/β.Cell reports · 2022Article
- Tuning Formation of Protein-DNA Coacervates by Sequence and Environment.The journal of physical chemistry. B · 2022Article
- Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma.Biophysics reviews · 2022Review
- Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases.Computational and structural biotechnology journal · 2022Article
- Structural Details of BH3 Motifs and BH3-Mediated Interactions: an Updated Perspective.Frontiers in molecular biosciences · 2022Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Intrinsically disordered proteins (IDP) are abundant in the human genome and have recently emerged as major therapeutic targets for various diseases. Unlike traditional proteins that adopt a definitive structure, IDPs in free solution are disordered and exist as an ensemble of conformations. This enables the IDPs to signal through multiple signaling pathways and serve as scaffolds for multi-protein complexes. The challenge in studying IDPs experimentally stems from their disordered nature. Nuclear magnetic resonance (NMR), circular dichroism, small angle X-ray scattering, and single molecule Förster resonance energy transfer (FRET) can give the local structural information and overall dimension of IDPs, but seldom provide a unified picture of the whole protein. To understand the conformational dynamics of IDPs and how their structural ensembles recognize multiple binding partners and small molecule inhibitors, knowledge-based and physics-based sampling techniques are utilized in-silico, guided by experimental structural data. However, efficient sampling of the IDP conformational ensemble requires traversing the numerous degrees of freedom in the IDP energy landscape, as well as force-fields that accurately model the protein and solvent interactions. In this review, we have provided an overview of the current state of computational methods for studying IDP structure and dynamics and discussed the major challenges faced in this field.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.