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Gaetano T. Montelione Laboratory
CABM Protein NMR Laboratory

Software

CABM AutoNMR Software

A powerful feature of macromolecular structure analysis by NMR spectroscopy is its potential for automation. A critical next step in evolving a level of scientific maturity in the field of biomolecular NMR is to establish conventions and standards of data interpretation and validation, and to instantiate these standards as part of a largely automated process of data analysis. The following software, developed in the Center for Advanced Biotechnology (CABM) and Medicine at Rutgers University, has addresses key issues of automated NMR data analysis

Standardized Protein NMR Information Storage

SPINS (Standardized ProteIn Nmr Storage) software is a Laboratory Information Management System (LIMS) aimed at organizing NMR structure determination projects and seamlessly exporting that information to the public database. The software tracks intermediate files during each step of the structure determination process including: data collection, data processing, resonance assignments, and structure calculation.

Automated NMR Resonance Assignments

AutoAssign is a constraint-based expert system designed to determine backbone HN, Ha, 13C', 13Ca, 15N, and 13Cb resonance assignments from peak lists derived from a set of triple resonance spectra with common HN-15N resonance correlations. Using the AutoAssign software, complete backbone resonance assignments are now routinely made within hours of completing the final data acquisition.

Automated NOESY Data Analysis

AutoStructure is automated protein structure determination software which involves iterative analysis of multidimensional NOESY data. Using AutoStructure in combination with the structure calculation software DYANA, CNS/XPLOR, and a multi-CPU cluster, protein structures can be calculated within hours. To date over twenty proteins have been deposited in the public database using the AutoStructure method.

Zimmerman, D.E.; Kulikowski, C.A.; Feng, W.; Tashiro, M.; Chien, C-Y.; Ríos, C.B.; Moy, F.J.; Powers, R.; Montelione G.T. J. Mol. Biol. 1997, 269: 592 - 610. Artificial intelligence methods for automated analysis of protein resonance assignments.

Moseley, H. N. B. and Montelione, G. T. Curr. Opin. Struct. Biol. 1999, 9: 635 - 642. Automated analysis of NMR assignments and structures for proteins.

Moseley, H.N.B.; Monleon, D.; Montelione, G.T. Meth. Enzymology 2001, 339: 91-108. Automatic determination of protein backbone resonance assignments from triple-resonance NMR data.

Baran, M.; Moseley, H.N.B.; Sahota, G.; Montelione, G.T. J. Biomol. NMR 2002, 24: 113-121. SPINS: Standardized ProteIn NMR Storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra.

Moseley, H.N.B.; Sahota, G.; Montelione, G.T. J. Biomol. NMR 2004, 28: 341-355. Assignment validation software suite for the evaluation and presentation of protein resonance assignment data.

Baran, M.C.; Huang, Y.J.; Moseley, H.N.; Montelione, G.T. Chemical Reviews 2004, 104: 3451-3555. Automated analysis of protein NMR assignments and structures.

Huang, Y.J.; Moseley, H.N.B.; Baran, M.C.; Arrowsmith, C.; Powers, R.; Tejero, R.; Szyperski, T.; Montelione, G.T. Meth. Enzymology 2005, 394: 111-141. An integrated platform for automated analysis of protein NMR structures.

Huang, Y.J.; Powers, R.; Montelione, G.T. J. Amer. Chem. Soc. 2005, 127: 1665-74. Protein NMR Recall, Precision, and F-measure scores (RPF Scores): Structure quality assessment measures based on information retrieval statistics.