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ProDy is a free and open-source Python package for analysis and modeling of protein structural dynamics. It allows for efficient analysis of large datasets and is suitable for development or prototyping of structure-based analysis and modeling software.

A simple web front end to NCBI BLAST+ that lets users share, and consume sequence data intuitively. "The iPod of Blast searching" Set up your local BLAST server in minutes...

Proteomatic is a free data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments. Functionality is provided via scripts, and these scripts can be chained together into a high-throughput data processing pipeline. All functionality can be used either ... [More] from the command-line or via a GUI (graphical user interface). Proteomatic automatically downloads necessary software packages such as OMSSA or BLAST when they are required, so it’s easy to get up and running. Proteomatic is available for Windows, Mac OS X and Linux. [Less]