ArticleProtein science : a publication of the Protein Society2018
PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode.
Article in Protein science : a publication of the Protein Society, 2018. 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 16 papers.
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Who cites it
16 citing papers in PubMed.
- Superwater as a generative AI framework to predict water molecule positions on protein structures.Communications chemistry · 2025Article
- A hybrid evolutionary and structural method for AI-guided peptide inhibitor design using AlphaFold and Rosetta.Scientific reports · 2025Article
- A Paired Database of Predicted and Experimental Protein Peptide Binding Information.Scientific data · 2025Article
- Design of target specific peptide inhibitors using generative deep learning and molecular dynamics simulations.Nature communications · 2024Article
- A Structure-based Data Set of Protein-peptide Affinities and its Nonredundant Benchmark: Potential Applications in Computational Peptidology.Current medicinal chemistry · 2024Article
- Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data.Scientific data · 2023Article
- DisCanVis: Visualizing integrated structural and functional annotations to better understand the effect of cancer mutations located within disordered proteins.Protein science : a publication of the Protein Society · 2023Article
- Tertiary motifs as building blocks for the design of protein-binding peptides.Protein science : a publication of the Protein Society · 2022Article
- Prediction and Modeling of Protein-Protein Interactions Using "Spotted" Peptides with a Template-Based Approach.Biomolecules · 2022Article
- Structural Features of Antibody-Peptide Recognition.Frontiers in immunology · 2022Article
- Modelling peptide-protein complexes: docking, simulations and machine learning.QRB discovery · 2022Article
- Propedia: a database for protein-peptide identification based on a hybrid clustering algorithm.BMC bioinformatics · 2021Article
- Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45.Proteins · 2020Article
- Structural and computational examination of theThe Journal of biological chemistry · 2019Article
- Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1.Structure (London, England : 1993) · 2019Article
- The cell cycle regulator GpsB functions as cytosolic adaptor for multiple cell wall enzymes.Nature communications · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
PixelDB, the Peptide Exosite Location Database, compiles 1966 non-redundant, high-resolution structures of protein-peptide complexes filtered to minimize the impact of crystal packing on peptide conformation. The database is organized to facilitate study of structurally conserved versus non-conserved elements of protein-peptide engagement. PixelDB clusters complexes based on the structural similarity of the peptide-binding protein, and by comparing complexes within a cluster highlights examples of domains that engage peptides using more than one binding mode. PixelDB also identifies conserved peptide core structural motifs characteristic of each binding mode. Peptide regions that flank core motifs often make non-structurally conserved interactions with the protein surface in regions we call exosites. Many examples establish that exosite contacts can be important for enhancing protein binding and interaction specificity. PixelDB provides a resource for computational and structural biologists to study, model, and predict core-motif and exosite-contacting peptide interactions. PixelDB is available to the community without restriction in a convenient flat-file format with accompanying visualization tools.
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