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Sequence annotation visualization software tools | Protein structure data analysis

Modern techniques have produced many sequence annotation databases and protein structure portals, but these Web resources are rarely integrated in ways that permit straightforward exploration of protein functional residues and their co-localization.

Source text:
(Mielke et al., 2014) AMASS: a database for investigating protein structures. Bioinformatics.

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Aquaria
A publicly available web resource that streamlines and simplifies the process of gleaning insight from protein structures. In contrast to most molecular graphics tools, the user interface of Aquaria is organized primarily by protein sequence, not structure. A user starts by specifying a protein of interest by name and organism, by identifier or by URL; Aquaria then generates a concise visual summary of all related PDB structures, using a precalculated all-against-all comparison of Swiss-Prot and PDB sequences (updated monthly). Aquaria is designed for biologists; its user interface creates clear and useful default views that show only the most relevant structural information tightly integrated with sequence, features and text that provide biological context.
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ProSAT / Protein Structure Annotation Tool-plus
A web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT+ incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing.
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PyMOL
Generates high-quality publication-ready molecular graphics images and animations. PyMOL is a molecular graphics system targeted at medium to large biomolecules like proteins. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. It includes visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals, molecular builder and sculptor, internal raytracer and movie generator.
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Gabedit
A freeware graphical user interface that offers preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. Gabedit includes tools for editing, displaying, analyzing, converting, and animating molecular systems. It can generate a Povray file for geometry, surfaces, contours, and color-coded planes. This tool is developed to facilitate the production of results from quantum chemistry methods through various computational chemistry software (CCS) and to provide a thorough analysis of these results.
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