AutoStructure is a protein structure determination tool that uses uninterpreted NOESY cross peaks together with structure calculation programs like XPLOR or DYANA to generate a 3D structure of the protein that is as close to the true structure as possible. AutoStructure uses an iterative bottom-up topology-constrained approach to analyze NOE peak lists. It first builds an initial fold based on intraresidue and sequential NOESY data, together with characteristic NOE patterns of secondary structures, including helical medium-range NOE interactions and interstrand beta-sheet NOE interactions, and unique long-range packing NOE interactions based on chemical shift matching and symmetry considerations. Unassigned NOESY cross peaks are not used in structure calculations. Additional NOESY cross peaks are iteratively assigned using intermediate structures and the knowledge of high-order topology constraints of alpha-helix and beta-sheet packing geometries. This protocol, in principal, resembles the methodology that an expert would utilize in manually solving a protein structure by NMR.

RPF uses a novel, rapid, and simple approach for calculating global structure quality scores. Specifically, this program calculates RECALL, PRECISION, and F-MEASURE (RPF) scores for the query structures, which are statistical quality scores commonly used in the field of information retrieval. These scores quickly provide the goodness-of-fit of the query structures when compared to the NOESY peak lists and resonance assignment data. The program also presents false positive and false negative data that can be used in refining the NMR structure determination protocols.

The input for AutoStructure/RPF includes the amino acid sequence, a list of resonance assignments, lists of 2D, 3D, and/or 4D-NOESY cross peaks. Query structure(s) are needed for RPF.

AutoStructure/RPF is only available for Redhat Linux platform.

Version 2.1.1 with GUI interface has been released on 2006-2-28.

You can download a license agreement (in pdf format). The distribution includes Hyper, PDBStat, and RPF as part of the AutoStructure software package.

Huang, Y. J.; Tejero, R.; Powers, R.; Montelione, G.T. A topology-constrained distance network algorithm for protein structure determination from NOESY data. PROTEINS: Struct. Funct. Bioinformatics 15, 587-603 (2006)

Huang, Y. J.; Powers, R. & Montelione, G. T. Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127, 1665-74 (2005)