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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

REPOSITORIES: biostudies-literature

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

Gajda Michał Jan MJ

BMC research notes 20131123

<h4>Background</h4>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.<h4>Findings</h4>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 program ...[more]

PMID: 24267035

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