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. © 2013 Gajda; licensee BioMed Central Ltd.