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Bioinformatics
Article . 2023 . Peer-reviewed
License: CC BY
Data sources: Crossref
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Bioinformatics
Article . 2023
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https://doi.org/10.1101/2022.1...
Article . 2022 . Peer-reviewed
Data sources: Crossref
DBLP
Article . 2024
Data sources: DBLP
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TALAIA: a 3D visual dictionary for protein structures

Authors: Mercè Alemany-Chavarria; Jaime Rodríguez-Guerra; Jean-Didier Maréchal;

TALAIA: a 3D visual dictionary for protein structures

Abstract

Abstract Motivation Graphical analysis of the molecular structure of proteins can be very complex. Full-atom representations retain most geometric information but are generally crowded, and key structural patterns can be challenging to identify. Non-full-atom representations could be more instructive on physicochemical aspects but be insufficiently detailed regarding shapes (e.g. entity beans-like models in coarse grain approaches) or simple properties of amino acids (e.g. representation of superficial electrostatic properties). In this work, we present TALAIA a visual dictionary that aims to provide another layer of structural representations. TALAIA offers a visual grammar that combines simple representations of amino acids while retaining their general geometry and physicochemical properties. It uses unique objects, with differentiated shapes and colors to represent amino acids. It makes easier to spot crucial molecular information, including patches of amino acids or key interactions between side chains. Most conventions used in TALAIA are standard in chemistry and biochemistry, so experimentalists and modelers can rapidly grasp the meaning of any TALAIA depiction. Results We propose TALAIA as a tool that renders protein structures and encodes structure and physicochemical aspects as a simple visual grammar. The approach is fast, highly informative, and intuitive, allowing the identification of possible interactions, hydrophobic patches, and other characteristic structural features at first glance. The first implementation of TALAIA can be found at https://github.com/insilichem/talaia.

Country
Spain
Keywords

Applications Note, Proteins, Amino Acids, Hydrophobic and Hydrophilic Interactions

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
1
Average
Average
Average
Green
gold