ArticleNature biotechnology2008
Predicting PDZ domain-peptide interactions from primary sequences.
Article in Nature biotechnology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 79 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.
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Who cites it
79 citing papers in PubMed, 131 citations in OpenAlex.
- Afadin couples RAS GTPases to the polarity rheostat Scribble.Nature communications · 2022Article
- Structure-conditioned amino-acid couplings: How contact geometry affects pairwise sequence preferences.Protein science : a publication of the Protein Society · 2022Article
- Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Functionalization of Cellulose-Based Hydrogels with Bi-Functional Fusion Proteins Containing Carbohydrate-Binding Modules.Materials (Basel, Switzerland) · 2021Article
- Article
- A Fluorescence-Based Assay to Determine PDZ-Ligand Binding Thermodynamics.Methods in molecular biology (Clifton, N.J.) · 2021Article
- New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data.The Journal of biological chemistry · 2020Article
- Emerging Themes in PDZ Domain Signaling: Structure, Function, and Inhibition.International review of cell and molecular biology · 2019Review
- Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling.Journal of biosciences · 2018Review
- Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions.Structure (London, England : 1993) · 2016Article
- Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast.Bioinformatics (Oxford, England) · 2016Article
- Insights into the C-terminal Peptide Binding Specificity of the PDZ Domain of Neuronal Nitric-oxide Synthase: CHARACTERIZATION OF THE INTERACTION WITH THE TIGHT JUNCTION PROTEIN CLAUDIN-3.The Journal of biological chemistry · 2016Article
- MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.Bioinformatics (Oxford, England) · 2016Article
- The Functional Human C-Terminome.PloS one · 2016Article
- Adaptable hydrogel networks with reversible linkages for tissue engineering.Advanced materials (Deerfield Beach, Fla.) · 2015Review
- SORTCERY-A High-Throughput Method to Affinity Rank Peptide Ligands.Journal of molecular biology · 2015Article
- Learning sequence determinants of protein:protein interaction specificity with sparse graphical models.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- Predicting peptide-mediated interactions on a genome-wide scale.PLoS computational biology · 2015Article
- Data-driven prediction and design of bZIP coiled-coil interactions.PLoS computational biology · 2015Article
- Computational design of selective peptides to discriminate between similar PDZ domains in an oncogenic pathway.Journal of molecular biology · 2015Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
PDZ domains constitute one of the largest families of interaction domains and function by binding the C termini of their target proteins. Using Bayesian estimation, we constructed a three-dimensional extension of a position-specific scoring matrix that predicts to which peptides a PDZ domain will bind, given the primary sequences of the PDZ domain and the peptides. The model, which was trained using interaction data from 82 PDZ domains and 93 peptides encoded in the mouse genome, successfully predicts interactions involving other mouse PDZ domains, as well as PDZ domains from Drosophila melanogaster and, to a lesser extent, PDZ domains from Caenorhabditis elegans. The model also predicts the differential effects of point mutations in peptide ligands on their PDZ domain-binding affinities. Overall, we show that our approach captures, in a single model, the binding selectivity of the PDZ domain family.
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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.