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Utopia Documents can be used in the same way as any other PDF reader, such as Adobe Acrobat Reader or the Preview application on a Mac. The application's workspace is split into three main panes (which can be collapsed): the PDF file itself is displayed on the left, a 'pager' is displayed at the bottom, and a sidebar to the right.
UTOPIA (User-friendly Tools for Operating Informatics Applications) is a suite of free tools for visualising and analysing bioinformatics data. Based on an ontology-driven data model, it contains applications for viewing and aligning protein sequences, rendering complex molecular structures in 3D, and for finding and using resources such as web services and data objects.
It is a web-based, open source user interface for analyzing and displaying protein identification data. It was originally designed by Rob Craig and Ron Beavis and first released in 2003. [ 1 ] The interface creates a series of web browser page views of tandem mass spectrometry data that has been assigned to protein sequences.
LeDock is a molecular docking software, designed for protein-ligand interactions, that is compatible with Linux, macOS, and Windows. [2] [3] [4] The software can run as a standalone programme or from Jupyter Notebook. [5] It supports the Tripos Mol2 file format.
A fingerprint is a group of conserved motifs taken from a multiple sequence alignment - together, the motifs form a characteristic signature for the aligned protein family. The motifs themselves are not necessarily contiguous in sequence, but may come together in 3D space to define molecular binding sites or interaction surfaces.
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MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is a computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain . The method was published by Robert C. Edgar in two papers in 2004.
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