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An algebraic geometry approach to protein structure determination from NMR data

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3 Author(s)
L. Wang ; Dept. of Comput. Sci., Dartmouth Coll., Hanover, NH, USA ; R. R. Mettu ; B. R. Donald

Our paper describes the first provably-efficient algorithm for determining protein structures de novo, solely from experimental data. We show how the global nature of a certain kind of NMR data provides quantifiable complexity-theoretic benefits, allowing us to classify our algorithm as running in polynomial time. While our algorithm uses NMR data as input, it is the first polynomial-time algorithm to compute high-resolution structures de novo using any experimentally-recorded data, from either NMR spectroscopy or X-Ray crystallography. Improved algorithms for protein structure determination are needed, because currently, the process is expensive and time-consuming. In our algorithm, RDC (residual dipolar coupling) data, which gives global restraints on the orientation of internuclear bond vectors, is used in conjunction with very sparse NOE data to obtain a polynomial-time algorithm for protein structure determination. An implementation of our algorithm has been applied to 6 different real biological NMR data sets recorded for 3 proteins. Our algorithm is combinatorially precise, polynomial-time, and uses much less NMR data to produce results that are as good or better than previous approaches in terms of accuracy of the computed structure as well as running time. In practice approaches such as restrained molecular dynamics and simulated annealing, which lack both combinatorial precision and guarantees on running time and solution quality, are commonly used. Our results show that by using a different "slice" of the data, an algorithm that is polynomial time and that has guarantees about solution quality can be obtained. We believe that our techniques can be. extended and generalized for other structure-determination problems such as computing side-chain conformations and the structure of nucleic acids from experimental data.

Published in:

2005 IEEE Computational Systems Bioinformatics Conference (CSB'05)

Date of Conference:

8-11 Aug. 2005