ArticleNucleic acids research2015
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed, 24 citations in OpenAlex.
- Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach.Journal of cheminformatics · 2026Article
- Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.Nucleic acids research · 2021Article
- High-performance macromolecular data delivery and visualization for the web.Acta crystallographica. Section D, Structural biology · 2020Article
- 3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns.International journal of molecular sciences · 2019Article
- MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).Nucleic acids research · 2018Article
- LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data.Nature methods · 2017Article
- Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes.Scientific reports · 2017Article
- Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL.PloS one · 2017Article
- The Eighth Central European Conference "Chemistry towards Biology": Snapshot.Molecules (Basel, Switzerland) · 2016Article
- Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach.Journal of cheminformatics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data. The extraction generally takes a few seconds for several hundreds of entries, up to approximately one hour for the whole PDB. The detected patterns are made available for download to enable further processing, as well as presented in a clear tabular and graphical form directly in the browser. The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. The application is available free of charge at http://ncbr.muni.cz/PatternQuery.
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.