HPDB-Haskell library for processing atomic biomolecular structures in Protein Data Bank format.

ABSTRACT:

Background

Protein DataBank file format is used for the majority of biomolecular data available today. Haskell is a lazy functional language that enjoys a high-level class-based type system, a growing collection of useful libraries and a reputation for efficiency.

Findings

I present a fast library for processing biomolecular data in the Protein Data Bank format. I present benchmarks indicating that this library is faster than other frequently used Protein Data Bank parsing programs. The proposed library also features a convenient iterator mechanism, and a simple API modeled after BioPython.

Conclusion

I set a new standard for convenience and efficiency of Protein Data Bank processing in a Haskell library, and release it to open source.

SUBMITTER: Gajda MJ 

PROVIDER: S-EPMC3879085 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature