ProDy makes use of the following great software:

pyparsing is used to define the sophisticated atom selection grammar. This makes every user a power user by enabling fast access to and easy handling of atomic data via simple selection statements.

Biopython KDTree package and TreeConstruction module, which are distributed ProDy, significantly enrich and improve the ProDy user experience. KDtree package allows for fast distance based selections making atom selections suitable for contact identification. TreeConstruction module enables the calculation of phylogenetic trees.

ProDy requires NumPy for almost all major functionality including, but not limited to, storing atomic data and performing normal mode calculations. The power and speed of NumPy makes ProDy suitable for interactive and high-throughput structural analysis.

CEalign is distributed with ProDy. The original CE method was developed by Ilya Shindyalov and Philip Bourne. The Python version which is used by ProDy is developed by Jason Vertrees and available under the New BSD license.

Finally, ProDy can benefit from SciPy and Matplotlib packages. SciPy makes ProDy normal calculations more flexible and on low memory machines possible. Matplotlib allows greatly enriches user experience by allowing plotting protein dynamics data calculated using ProDy.