Evidence map›Paper›PMID 25425036›Full record

ArticleDatabase : the journal of biological databases and curation2014

Small molecule annotation for the Protein Data Bank.

Sanchayita Sen, Jasmine Young, John M Berrisford, Minyu Chen, Matthew J Conroy, Shuchismita Dutta, Luigi Di Costanzo, Guanghua Gao, Sutapa Ghosh, Brian P Hudson and 13 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
4.4field-weighted citation impact, top 5% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 32 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Additive CHARMM36 Force Field for Nonstandard Amino Acids.Journal of chemical theory and computation · 2021
    Article
  8. Building and rebuilding N-glycans in protein structure models.Acta crystallographica. Section D, Structural biology · 2019
    Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Estimation of the protein-ligand interaction energy for model building and validation.Acta crystallographica. Section D, Structural biology · 2017
    Article
  14. Article
  15. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.Structure (London, England : 1993) · 2016
    Article
  16. Progress in protein crystallography.Protein and peptide letters · 2016
    Article
  17. Article
  18. Many InChIs and quite some feat.Journal of computer-aided molecular design · 2015
    Article
  19. Article
  20. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

23 authors at 1 institution in 1 country.

Sanchayita SenProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan ssen@ebi.ac.uk.
Jasmine YoungProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
John M BerrisfordProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Minyu ChenProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Matthew J ConroyProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Shuchismita DuttaProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Luigi Di CostanzoProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Guanghua GaoProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Sutapa GhoshProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Brian P HudsonProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Reiko IgarashiProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Yumiko KengakuProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Yuhe LiangProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Ezra PeisachProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Irina PersikovaProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Abhik MukhopadhyayProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Buvaneswari Coimbatore NarayananProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Gaurav SahniProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Junko SatoProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Monica SekharanProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Chenghua ShaoProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Lihua TanProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Marina A ZhuravlevaProtein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan.
Rutgers, The State University of New Jersey · US

Funding

Biotechnology and Biological Sciences Research Council BB/I02576X/1Biotechnology and Biological Sciences Research Council BB/J007471/1Biotechnology and Biological Sciences Research Council BB/K016970/1Wellcome Trust 088944
6 · The paper itself

Abstract

The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.

Indexed as

Databases, ChemicalDatabases, ProteinAnti-Bacterial AgentsBinding SitesData MiningGlucoseGlycopeptidesLigandsModels, MolecularReproducibility of ResultsSmall Molecule LibrariesAnti-Bacterial AgentsGlucoseGlycopeptidesLigandsSmall Molecule Libraries

Identifiers

PMID25425036
PMCPMC4243272
OpenAlexW2040535930

What OpenQuestion holds

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Registered trials

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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.