ArticlePLoS computational biology2020
Sequence-based prediction of protein binding mode landscapes.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 62 citations in OpenAlex.
- Prevalence and Functional Roles of Intrinsic Disorder in the [F-actin]-monooxygenase MICAL Family Members and their Interactors.Cell biochemistry and biophysics · 2026Article
- FuzDrop: sequence-based prediction of the propensity of proteins for liquid-liquid phase separation and aggregation.Nature protocols · 2026Review
- Integrated Symbiotic Pleiotropy: Long Non-Coding RNAs and Disordered Proteins Interweaving the Functional Layers of the Eukaryotic Cell.International journal of molecular sciences · 2026Review
- LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank.Genomics, proteomics & bioinformatics · 2025Article
- Multivalent interaction induces phase separation and formation of more toxic aggregates of α-syn in a yeast model of Parkinson's disease.Protein science : a publication of the Protein Society · 2025Article
- An Analysis of Intrinsic Protein Disorder in Antimicrobial Peptides.The protein journal · 2025Article
- Cellular RNA interacts with MAVS to promote antiviral signaling.Science (New York, N.Y.) · 2024Article
- Structural study of the intrinsically disordered tardigrade damage suppressor protein (Dsup) and its complex with DNA.Scientific reports · 2024Article
- Oncogenic p53 triggers amyloid aggregation of p63 and p73 liquid droplets.Communications chemistry · 2024Article
- Intrinsic disorder in the human vitreous proteome.International journal of biological macromolecules · 2024Article
- Deep mutational scanning of the RNase III-like domain inFrontiers in cellular and infection microbiology · 2024Article
- CELLULAR RNA INTERACTS WITH MAVS TO PROMOTE ANTIVIRAL SIGNALING.bioRxiv : the preprint server for biology · 2023Article
- Protein nanocondensates: the next frontier.Biophysical reviews · 2023Review
- FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins.Nucleic acids research · 2023Article
- Biomolecular condensates: insights into early and late steps of the HIV-1 replication cycle.Retrovirology · 2023Review
- Article
- MobiDB: 10 years of intrinsically disordered proteins.Nucleic acids research · 2023Article
- Protein interactions: anything new?Essays in biochemistry · 2022Article
- SH2 Domains: Folding, Binding and Therapeutical Approaches.International journal of molecular sciences · 2022Review
- Sequence-based Prediction of the Cellular Toxicity Associated with Amyloid Aggregation within Protein Condensates.Biochemistry · 2022Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Interactions between disordered proteins involve a wide range of changes in the structure and dynamics of the partners involved. These changes can be classified in terms of binding modes, which include disorder-to-order (DO) transitions, when proteins fold upon binding, as well as disorder-to-disorder (DD) transitions, when the conformational heterogeneity is maintained in the bound states. Furthermore, systematic studies of these interactions are revealing that proteins may exhibit different binding modes with different partners. Proteins that exhibit this context-dependent binding can be referred to as fuzzy proteins. Here we investigate amino acid code for fuzzy binding in terms of the entropy of the probability distribution of transitions towards decreasing order. We implement these entropy calculations into the FuzPred (http://protdyn-fuzpred.org) algorithm to predict the range of context-dependent binding modes of proteins from their amino acid sequences. As we illustrate through a variety of examples, this method identifies those binding sites that are sensitive to the cellular context or post-translational modifications, and may serve as regulatory points of cellular pathways.
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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.