Lemon: a framework for rapidly mining structural information from the Protein Data Bank | Zendy

Jonathan Fine | Zendy; Gaurav Chopra | Zendy

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Lemon: a framework for rapidly mining structural information from the Protein Data Bank

Author(s) -

Jonathan Fine,

Gaurav Chopra

Publication year - 2019

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btz178

Subject(s) - protein data bank (rcsb pdb) , python (programming language) , protein data bank , parsing , computer science , scripting language , structural bioinformatics , software , workflow , header , benchmarking , collaboratory , suite , uniprot , data mining , programming language , database , protein structure , world wide web , biology , history , computer network , biochemistry , archaeology , marketing , gene , business

The Protein Data Bank (PDB) currently holds over 140 000 biomolecular structures and continues to release new structures on a weekly basis. The PDB is an essential resource to the structural bioinformatics community to develop software that mine, use, categorize and analyze such data. New computational biology methods are evaluated using custom benchmarking sets derived as subsets of 3D experimentally determined structures and structural features from the PDB. Currently, such benchmarking features are manually curated with custom scripts in a non-standardized manner that results in slow distribution and updates with new experimental structures. Finally, there is a scarcity of standardized tools to rapidly query 3D descriptors of the entire PDB.

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