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NLDB: a database for 3D protein–ligand interactions in enzymatic reactions

Overview of attention for article published in Journal of Structural and Functional Genomics, August 2016
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (56th percentile)

Mentioned by

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5 tweeters

Citations

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1 Dimensions

Readers on

mendeley
11 Mendeley
Title
NLDB: a database for 3D protein–ligand interactions in enzymatic reactions
Published in
Journal of Structural and Functional Genomics, August 2016
DOI 10.1007/s10969-016-9206-0
Pubmed ID
Authors

Yoichi Murakami, Satoshi Omori, Kengo Kinoshita

Abstract

NLDB (Natural Ligand DataBase; URL: http://nldb.hgc.jp ) is a database of automatically collected and predicted 3D protein-ligand interactions for the enzymatic reactions of metabolic pathways registered in KEGG. Structural information about these reactions is important for studying the molecular functions of enzymes, however a large number of the 3D interactions are still unknown. Therefore, in order to complement such missing information, we predicted protein-ligand complex structures, and constructed a database of the 3D interactions in reactions. NLDB provides three different types of data resources; the natural complexes are experimentally determined protein-ligand complex structures in PDB, the analog complexes are predicted based on known protein structures in a complex with a similar ligand, and the ab initio complexes are predicted by docking simulations. In addition, NLDB shows the known polymorphisms found in human genome on protein structures. The database has a flexible search function based on various types of keywords, and an enrichment analysis function based on a set of KEGG compound IDs. NLDB will be a valuable resource for experimental biologists studying protein-ligand interactions in specific reactions, and for theoretical researchers wishing to undertake more precise simulations of interactions.

Twitter Demographics

The data shown below were collected from the profiles of 5 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 11 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 11 100%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 4 36%
Other 2 18%
Student > Master 1 9%
Student > Ph. D. Student 1 9%
Researcher 1 9%
Other 1 9%
Unknown 1 9%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 4 36%
Agricultural and Biological Sciences 2 18%
Pharmacology, Toxicology and Pharmaceutical Science 1 9%
Unspecified 1 9%
Chemistry 1 9%
Other 1 9%
Unknown 1 9%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 04 September 2016.
All research outputs
#6,650,967
of 12,321,253 outputs
Outputs from Journal of Structural and Functional Genomics
#60
of 94 outputs
Outputs of similar age
#110,537
of 265,833 outputs
Outputs of similar age from Journal of Structural and Functional Genomics
#2
of 2 outputs
Altmetric has tracked 12,321,253 research outputs across all sources so far. This one is in the 44th percentile – i.e., 44% of other outputs scored the same or lower than it.
So far Altmetric has tracked 94 research outputs from this source. They receive a mean Attention Score of 3.1. This one is in the 35th percentile – i.e., 35% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 265,833 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 56% of its contemporaries.
We're also able to compare this research output to 2 others from the same source and published within six weeks on either side of this one.