ArticleNucleic acids research2011
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Deep Learning in Phosphoproteomics: Methods and Application in Cancer Drug Discovery.Proteomes · 2023Review
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteins.Physical chemistry chemical physics : PCCP · 2022Review
- Current status of PTMs structural databases: applications, limitations and prospects.Amino acids · 2022Review
- Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources.Clinical proteomics · 2020Review
- The Complex Phosphorylation Patterns that Regulate the Activity of Hsp70 and Its Cochaperones.International journal of molecular sciences · 2019Review
- AWESOME: a database of SNPs that affect protein post-translational modifications.Nucleic acids research · 2019Article
- Preparation of Phosphorylated Proteins for NMR Spectroscopy.Methods in enzymology · 2019Article
- Application of Proteomics Technologies in Oil Palm Research.The protein journal · 2018Review
- Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones.Scientific reports · 2018Article
- Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.BMC systems biology · 2017Article
- PredPhos: an ensemble framework for structure-based prediction of phosphorylation sites.Journal of biological research (Thessalonike, Greece) · 2016Article
- Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.PLoS computational biology · 2015Article
- Structural Analysis of PTM Hotspots (SAPH-ire)--A Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families.Molecular & cellular proteomics : MCP · 2015Article
- RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.Database : the journal of biological databases and curation · 2014Article
- Physicochemical mechanisms of protein regulation by phosphorylation.Frontiers in genetics · 2014Review
- PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.Database : the journal of biological databases and curation · 2014Article
- Evolution and functional cross-talk of protein post-translational modifications.Molecular systems biology · 2013Review
- Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures.BMC bioinformatics · 2013Article
- Phosphorylation variation during the cell cycle scales with structural propensities of proteins.PLoS computational biology · 2013Article
- Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis.Molecular bioSystems · 2012Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phospho3D is a database of three-dimensional (3D) structures of phosphorylation sites (P-sites) derived from the Phospho.ELM database, which also collects information on the residues surrounding the P-site in space (3D zones). The database also provides the results of a large-scale structural comparison of the 3D zones versus a representative dataset of structures, thus associating to each P-site a number of structurally similar sites. The new version of Phospho3D presents an 11-fold increase in the number of 3D sites and incorporates several additional features, including new structural descriptors, the possibility of selecting non-redundant sets of 3D structures and the availability for download of non-redundant sets of structurally annotated P-sites. Moreover, it features P3Dscan, a new functionality that allows the user to submit a protein structure and scan it against the 3D zones collected in the Phospho3D database. Phospho3D version 2.0 is available at: http://www.phospho3d.org/.
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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.