↓ Skip to main content

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints

Overview of attention for article published in BMC Bioinformatics, January 2015
Altmetric Badge

About this Attention Score

  • Average Attention Score compared to outputs of the same age

Mentioned by

twitter
2 tweeters

Citations

dimensions_citation
41 Dimensions

Readers on

mendeley
32 Mendeley
citeulike
1 CiteULike
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
An algorithm to enumerate all possible protein conformations verifying a set of distance constraints
Published in
BMC Bioinformatics, January 2015
DOI 10.1186/s12859-015-0451-1
Pubmed ID
Authors

Andrea Cassioli, Benjamin Bardiaux, Guillaume Bouvier, Antonio Mucherino, Rafael Alves, Leo Liberti, Michael Nilges, Carlile Lavor, Thérèse E Malliavin

Abstract

BackgroundThe determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only.ResultsIn order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations.ConclusionsWe described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three ¿-helical peptides.

Twitter Demographics

The data shown below were collected from the profiles of 2 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 32 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 2 6%
United States 1 3%
Germany 1 3%
Unknown 28 88%

Demographic breakdown

Readers by professional status Count As %
Researcher 10 31%
Student > Ph. D. Student 4 13%
Student > Master 4 13%
Student > Doctoral Student 3 9%
Professor 3 9%
Other 5 16%
Unknown 3 9%
Readers by discipline Count As %
Chemistry 8 25%
Computer Science 7 22%
Biochemistry, Genetics and Molecular Biology 5 16%
Mathematics 4 13%
Agricultural and Biological Sciences 4 13%
Other 0 0%
Unknown 4 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 03 February 2015.
All research outputs
#11,070,336
of 14,573,111 outputs
Outputs from BMC Bioinformatics
#4,242
of 5,420 outputs
Outputs of similar age
#176,095
of 282,508 outputs
Outputs of similar age from BMC Bioinformatics
#35
of 42 outputs
Altmetric has tracked 14,573,111 research outputs across all sources so far. This one is in the 20th percentile – i.e., 20% of other outputs scored the same or lower than it.
So far Altmetric has tracked 5,420 research outputs from this source. They receive a mean Attention Score of 4.9. This one is in the 16th percentile – i.e., 16% 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 282,508 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 32nd percentile – i.e., 32% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 42 others from the same source and published within six weeks on either side of this one. This one is in the 14th percentile – i.e., 14% of its contemporaries scored the same or lower than it.