ArticleNucleic acids research2011
PCDB: a database of protein conformational diversity.
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 14 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
14 citing papers in PubMed.
- D3PM: a comprehensive database for protein motions ranging from residue to domain.BMC bioinformatics · 2022Article
- ModFlex: Towards Function Focused Protein Modeling.Journal of molecular biology · 2021Article
- Metamorphic proteins: the Janus proteins of structural biology.Open biology · 2021Article
- Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures.Briefings in bioinformatics · 2019Article
- PDBFlex: exploring flexibility in protein structures.Nucleic acids research · 2016Article
- CCProf: exploring conformational change profile of proteins.Database : the journal of biological databases and curation · 2016Article
- ChSeq: A database of chameleon sequences.Protein science : a publication of the Protein Society · 2015Review
- PeptiSite: a structural database of peptide binding sites in 4D.Biochemical and biophysical research communications · 2014Article
- BeEP Server: Using evolutionary information for quality assessment of protein structure models.Nucleic acids research · 2013Article
- On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions.BMC genomics · 2012Article
- Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins.BMC structural biology · 2012Article
- Pocketome: an encyclopedia of small-molecule binding sites in 4D.Nucleic acids research · 2012Article
- Evolutionary dynamics on protein bi-stability landscapes can potentially resolve adaptive conflicts.PLoS computational biology · 2012Article
- The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.Nucleic acids research · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PCDB (http://www.pcdb.unq.edu.ar) is a database of protein conformational diversity. For each protein, the database contains the redundant compilation of all the corresponding crystallographic structures obtained under different conditions. These structures could be considered as different instances of protein dynamism. As a measure of the conformational diversity we use the maximum RMSD obtained comparing the structures deposited for each domain. The redundant structures were extracted following CATH structural classification and cross linked with additional information. In this way it is possible to relate a given amount of conformational diversity with different levels of information, such as protein function, presence of ligands and mutations, structural classification, active site information and organism taxonomy among others. Currently the database contains 7989 domains with a total of 36581 structures from 4171 different proteins. The maximum RMSD registered is 26.7 Å and the average of different structures per domain is 4.5.
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.