title: AUTOBA: automation of backbone assignment from HN(C)N suite of experiments.
abstract: Development of efficient strategies and automation represent important milestones of progress in rapid structure determination efforts in proteomics research. In this context, we present here an efficient algorithm named as AUTOBA (Automatic Backbone Assignment) designed to automate the assignment protocol based on HN(C)N suite of experiments. Depending upon the spectral dispersion, the user can record 2D or 3D versions of the experiments for assignment. The algorithm uses as inputs: (i) protein primary sequence and (ii) peak-lists from user defined HN(C)N suite of experiments. In the end, one gets H(N), (15)N, C(α) and C' assignments (in common BMRB format) for the individual residues along the polypeptide chain. The success of the algorithm has been demonstrated, not only with experimental spectra recorded on two small globular proteins: ubiquitin (76 aa) and M-crystallin (85 aa), but also with simulated spectra of 27 other proteins using assignment data from the BMRB.
authors.affiliation: Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Homi Bhabha Road, Colaba, Mumbai, India.
authors.forename: Aditi
authors.initials: A
authors.lastname: Borkar
authors.forename: Dinesh
authors.initials: D
authors.lastname: Kumar
authors.forename: Ramakrishna V
authors.initials: RV
authors.lastname: Hosur
mesh_terms: D000465:Algorithms; D002247:Carbon Isotopes / Q000737:chemistry; D009587:Nitrogen Isotopes / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D011522:Protons; D025801:Ubiquitin / Q000737:chemistry; D038201:alpha-Crystallins / Q000737:chemistry
chemical_list: D002247:Carbon Isotopes; D009587:Nitrogen Isotopes; D011506:Proteins; D011522:Protons; D025801:Ubiquitin; D038201:alpha-Crystallins