title: CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis.
abstract: Tuberculosis kills more than a million people annually and presents increasingly high levels of resistance against current first line drugs. Structural information about Mycobacterium tuberculosis (Mtb) proteins is a valuable asset for the development of novel drugs and for understanding the biology of the bacterium; however, only about 10% of the ∼4000 proteins have had their structures determined experimentally. The CHOPIN database assigns structural domains and generates homology models for 2911 sequences, corresponding to ∼73% of the proteome. A sophisticated pipeline allows multiple models to be created using conformational states characteristic of different oligomeric states and ligand binding, such that the models reflect various functional states of the proteins. Additionally, CHOPIN includes structural analyses of mutations potentially associated with drug resistance. Results are made available at the web interface, which also serves as an automatically updated repository of all published Mtb experimental structures. Its RESTful interface allows direct and flexible access to structures and metadata via intuitive URLs, enabling easy programmatic use of the models.
authors.affiliation: Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK and Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India bernardo@cryst.bioc.cam.ac.uk.
authors.forename: Bernardo
authors.initials: B
authors.lastname: Ochoa-Montaño
authors.affiliation: Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK and Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK and Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India.
authors.forename: Nishita
authors.initials: N
authors.lastname: Mohan
authors.affiliation: Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK and Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India.
authors.forename: Tom L
authors.initials: TL
authors.lastname: Blundell
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000378:metabolism; D030541:Databases, Genetic; D024881:Drug Resistance, Bacterial; D006801:Humans; D008954:Models, Biological; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D014376:Tuberculosis / Q000188:drug therapy / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D020543:Proteome
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