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bioRxiv · 10.1101/2022.11.28.517961

TALAIA: A 3D visual dictionary for protein structures

Alemany-Chavarria, M.·Rodriguez-Guerra Pedragal, J.·Marechal, J.-D.
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Abstract

SummaryGraphical analysis of the molecular structure of proteins can be very complex. Full atom representations retain most of the geometric information but are generally crowded and key structural patterns can be difficult to catch. 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 individualistic properties of amino acids (e.g., representation of superficial electrostatic properties). TALAIA aims at providing another layer of structural representations. It is a visual dictionary where each amino acid is represented by a unique object with differentiated shapes and colors. It makes it easier to spot important molecular information including patches of amino acids or key interactions between side chains. Most of the conventions used in TALAIA are common in chemistry and biochemistry so that experimentalists and modelers can rapidly grasp the meaning of any TALAIA depictions. MotivationThe aim of the work is to offer a visual grammar that combines simplistic representations of amino acids while retaining their general geometry and physicochemical properties. ResultsWe propose a tool that renders protein structures and encodes both structure and physicochemical aspects as a simple visual grammar. The approach is fast, highly informative, and simple, allowing the identification of possible interactions, hydrophobic patches, and other characteristic structural features at a simple glance. Availabilityhttps://github.com/insilichem/talaia Contactjeandidier.marechal@uab.cat

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Alemany-Chavarria, M., Rodriguez-Guerra Pedragal, J., Marechal, J.-D.. 2022-11-29. TALAIA: A 3D visual dictionary for protein structures. https://doi.org/10.1101/2022.11.28.517961

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