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VIPERdb2: an enhanced and web API enabled relational database for structural virology

Overview of attention for article published in Nucleic Acids Research, November 2008
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Title
VIPERdb2: an enhanced and web API enabled relational database for structural virology
Published in
Nucleic Acids Research, November 2008
DOI 10.1093/nar/gkn840
Pubmed ID
Authors

Mauricio Carrillo-Tripp, Craig M. Shepherd, Ian A. Borelli, Sangita Venkataraman, Gabriel Lander, Padmaja Natarajan, John E. Johnson, Charles L. Brooks, Vijay S. Reddy

Abstract

VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb(2), we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Phi-Psi (Phi-Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence-structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.

Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 144 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 9 6%
Mexico 3 2%
Italy 2 1%
Brazil 1 <1%
Germany 1 <1%
France 1 <1%
Peru 1 <1%
Unknown 126 88%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 41 28%
Researcher 23 16%
Student > Master 19 13%
Student > Doctoral Student 9 6%
Student > Bachelor 9 6%
Other 26 18%
Unknown 17 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 37 26%
Biochemistry, Genetics and Molecular Biology 27 19%
Physics and Astronomy 18 13%
Chemistry 11 8%
Engineering 8 6%
Other 20 14%
Unknown 23 16%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 20 April 2020.
All research outputs
#8,534,976
of 25,374,647 outputs
Outputs from Nucleic Acids Research
#13,661
of 27,550 outputs
Outputs of similar age
#37,471
of 105,686 outputs
Outputs of similar age from Nucleic Acids Research
#102
of 208 outputs
Altmetric has tracked 25,374,647 research outputs across all sources so far. This one is in the 43rd percentile – i.e., 43% of other outputs scored the same or lower than it.
So far Altmetric has tracked 27,550 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 7.1. This one is in the 24th percentile – i.e., 24% 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 105,686 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 17th percentile – i.e., 17% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 208 others from the same source and published within six weeks on either side of this one. This one is in the 11th percentile – i.e., 11% of its contemporaries scored the same or lower than it.