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An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)

Overview of attention for article published in PeerJ, May 2017
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  • Good Attention Score compared to outputs of the same age (69th percentile)
  • Above-average Attention Score compared to outputs of the same age and source (52nd percentile)

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Title
An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)
Published in
PeerJ, May 2017
DOI 10.7717/peerj.3327
Pubmed ID
Authors

Ranjan V. Mannige

Abstract

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom-the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide's conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone's internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the 'dead space' within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 35 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 35 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 14 40%
Researcher 5 14%
Student > Master 4 11%
Student > Doctoral Student 2 6%
Student > Bachelor 2 6%
Other 4 11%
Unknown 4 11%
Readers by discipline Count As %
Chemistry 13 37%
Biochemistry, Genetics and Molecular Biology 6 17%
Agricultural and Biological Sciences 3 9%
Materials Science 2 6%
Chemical Engineering 1 3%
Other 5 14%
Unknown 5 14%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 06 May 2019.
All research outputs
#5,938,066
of 22,971,207 outputs
Outputs from PeerJ
#4,909
of 13,381 outputs
Outputs of similar age
#94,015
of 310,608 outputs
Outputs of similar age from PeerJ
#171
of 359 outputs
Altmetric has tracked 22,971,207 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 13,381 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 17.3. This one has gotten more attention than average, scoring higher than 62% of its peers.
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 310,608 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 69% of its contemporaries.
We're also able to compare this research output to 359 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 52% of its contemporaries.