A topology‐constrained distance network algorithm for protein structure determination from NOESY data

Proteins: Structure, Function and Bioinformatics - Tập 62 Số 3 - Trang 587-603 - 2006
Yuanpeng J. Huang1, Roberto Tejero1, Robert Powers2, G.T. Montelione1,3
1Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey
2Department of Chemistry, University of Nebraska–Lincoln, Lincoln, Nebraska
3Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey

Tóm tắt

AbstractThis article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom‐up, topology‐constrained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology‐constrained distance network analysis algorithm and iteratively generates structures using the three‐dimensional (3D) protein structure calculation programs XPLOR/CNS or DYANA. The minimum input for AutoStructure includes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D‐NOESY cross peaks. AutoStructure can also analyze homodimeric proteins when X‐filtered NOESY experiments are available. The quality of input data and final 3D structures is evaluated using recall, precision, and F‐measure (RPF) scores, a statistical measure of goodness of fit with the input data. AutoStructure has been tested on three protein NMR data sets for which high‐quality structures have previously been solved by an expert, and yields comparable high‐quality distance constraint lists and 3D protein structures in hours. We also compare several protein structures determined using AutoStructure with corresponding homologous proteins determined with other independent methods. The program has been used in more than two dozen protein structure determinations, several of which have already been published. Proteins 2006. © 2005 Wiley‐Liss, Inc.

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Proteins: Structure, Function and Bioinformatics

Tập 62 Số 3

587-603

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