ArticlePLoS computational biology2017
Modeling disordered protein interactions from biophysical principles.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 59 citations in OpenAlex.
- Peptide-protein docking: from physics-based models to generative intelligence.Chemical communications (Cambridge, England) · 2026Review
- Metal-Coordination Specificity and Structural Dynamics of C. elegans Metallothionein I: Insights From 3D Modeling and MD Simulations.Proteins · 2026Article
- Evaluation of predictions of disordered binding regions in the CAID2 experiment.Computational and structural biotechnology journal · 2025Review
- Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.International journal of molecular sciences · 2024Article
- Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.Journal of molecular biology · 2024Article
- Assessment of Protein-Protein Docking Models Using Deep Learning.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints.bioRxiv : the preprint server for biology · 2023Article
- Construction of Histone-Protein Complex Structures by Peptide Growing.International journal of molecular sciences · 2023Article
- Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.Proteomics · 2023Article
- Review
- Computational prediction of disordered binding regions.Computational and structural biotechnology journal · 2023Review
- Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server.Methods in molecular biology (Clifton, N.J.) · 2023Article
- In silico optimization of RNA-protein interactions for CRISPR-Cas13-based antimicrobials.Biology direct · 2022Article
- Multi-level analysis of intrinsically disordered protein docking methods.Methods (San Diego, Calif.) · 2022Article
- Matching protein surface structural patches for high-resolution blind peptide docking.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma.Biophysics reviews · 2022Review
- Towards rational computational peptide design.Frontiers in bioinformatics · 2022Article
- Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2022Review
- LZerD webserver for pairwise and multiple protein-protein docking.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Disordered protein-protein interactions (PPIs), those involving a folded protein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important signaling and regulatory pathways. IDPs do not adopt a single dominant structure in isolation but often become ordered upon binding. To aid understanding of the molecular mechanisms of disordered PPIs, it is crucial to obtain the tertiary structure of the PPIs. However, experimental methods have difficulty in solving disordered PPIs and existing protein-protein and protein-peptide docking methods are not able to model them. Here we present a novel computational method, IDP-LZerD, which models the conformation of a disordered PPI by considering the biophysical binding mechanism of an IDP to a structured protein, whereby a local segment of the IDP initiates the interaction and subsequently the remaining IDP regions explore and coalesce around the initial binding site. On a dataset of 22 disordered PPIs with IDPs up to 69 amino acids, successful predictions were made for 21 bound and 18 unbound receptors. The successful modeling provides additional support for biophysical principles. Moreover, the new technique significantly expands the capability of protein structure modeling and provides crucial insights into the molecular mechanisms of disordered PPIs.
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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.