ArticleBriefings in bioinformatics2020
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact.
Article in Briefings in bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- AIPred: comprehensive prediction and analysis of non-histone acetylation via protein language model and interpretable machine learning.BMC biology · 2025Article
- Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025Article
- m6A-TCPred: a web server to predict tissue-conserved human mBMC bioinformatics · 2024Article
- MERITS: a web-based integratedBioinformatics advances · 2024Article
- PTM-Psi: A python package to facilitate the computational investigation of post-translational modification on protein structures and their impacts on dynamics and functions.Protein science : a publication of the Protein Society · 2023Article
- Characterization of Proteoform Post-Translational Modifications by Top-Down and Bottom-Up Mass Spectrometry in Conjunction with Annotations.Journal of proteome research · 2023Article
- AQcalc: A web server that identifies weak molecular interactions in protein structures.Protein science : a publication of the Protein Society · 2023Article
- pSuc-EDBAM: Predicting lysine succinylation sites in proteins based on ensemble dense blocks and an attention module.BMC bioinformatics · 2022Article
- iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets.Nucleic acids research · 2022Article
- Current status of PTMs structural databases: applications, limitations and prospects.Amino acids · 2022Review
- pSuc-FFSEA: Predicting Lysine Succinylation Sites in Proteins Based on Feature Fusion and Stacking Ensemble Algorithm.Frontiers in cell and developmental biology · 2022Article
- Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework.Briefings in bioinformatics · 2021Article
- INTEDE: interactome of drug-metabolizing enzymes.Nucleic acids research · 2021Article
- Recent Advances in Predicting Protein S-Nitrosylation Sites.BioMed research international · 2021Review
- ActiveDriverDB: Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update).Frontiers in cell and developmental biology · 2021Article
- m5CPred-SVM: a novel method for predicting m5C sites of RNA.BMC bioinformatics · 2020Article
- Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information.Genomics, proteomics & bioinformatics · 2020Article
- PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification.Frontiers in cell and developmental biology · 2020Article
- Positive-unlabelled learning of glycosylation sites in the human proteome.BMC bioinformatics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
Post-translational modifications (PTMs) play very important roles in various cell signaling pathways and biological process. Due to PTMs' extremely important roles, many major PTMs have been studied, while the functional and mechanical characterization of major PTMs is well documented in several databases. However, most currently available databases mainly focus on protein sequences, while the real 3D structures of PTMs have been largely ignored. Therefore, studies of PTMs 3D structural signatures have been severely limited by the deficiency of the data. Here, we develop PRISMOID, a novel publicly available and free 3D structure database for a wide range of PTMs. PRISMOID represents an up-to-date and interactive online knowledge base with specific focus on 3D structural contexts of PTMs sites and mutations that occur on PTMs and in the close proximity of PTM sites with functional impact. The first version of PRISMOID encompasses 17 145 non-redundant modification sites on 3919 related protein 3D structure entries pertaining to 37 different types of PTMs. Our entry web page is organized in a comprehensive manner, including detailed PTM annotation on the 3D structure and biological information in terms of mutations affecting PTMs, secondary structure features and per-residue solvent accessibility features of PTM sites, domain context, predicted natively disordered regions and sequence alignments. In addition, high-definition JavaScript packages are employed to enhance information visualization in PRISMOID. PRISMOID equips a variety of interactive and customizable search options and data browsing functions; these capabilities allow users to access data via keyword, ID and advanced options combination search in an efficient and user-friendly way. A download page is also provided to enable users to download the SQL file, computational structural features and PTM sites' data. We anticipate PRISMOID will swiftly become an invaluable online resource, assisting both biologists and bioinformaticians to conduct experiments and develop applications supporting discovery efforts in the sequence-structural-functional relationship of PTMs and providing important insight into mutations and PTM sites interaction mechanisms. The PRISMOID database is freely accessible at http://prismoid.erc.monash.edu/. The database and web interface are implemented in MySQL, JSP, JavaScript and HTML with all major browsers supported.
Indexed as
Identifiers
What OpenQuestion holds
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.