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High-throughput NMR structural biology can play an important role in structural genomics. We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of an homologous structure. These assignments are a prerequisite for probing protein-protein interactions , protein-ligand binding, and dynamics by NMR.(More)
We have derived a quartic equation for computing the direction of an internuclear vector from residual dipolar couplings (RDCs) measured in two aligning media, and two simple trigonometric equations for computing the backbone (phi,psi) angles from two backbone vectors in consecutive peptide planes. These equations make it possible to compute, exactly and in(More)
We describe an efficient algorithm for protein backbone structure determination from solution Nuclear Magnetic Resonance (NMR) data. A key feature of our algorithm is that it finds the conformation and orientation of secondary structure elements as well as the global fold in polynomial time. This is the first polynomial-time algorithm for de novo(More)
Nuclear Overhauser effect (NOE) distance restraints are the main experimental data from protein nuclear magnetic resonance (NMR) spectroscopy for computing a complete three dimensional solution structure including sidechain conformations. In general NOE restraints must be assigned before they can be used in a structure determination program. NOE assignment(More)
We have developed an ab initio algorithm for determining a protein backbone structure using global orientational restraints on internuclear vectors derived from residual dipolar couplings (RDCs) measured in one or two different aligning media by solution nuclear magnetic resonance (NMR) spectroscopy. Specifically, the conformation and global orientations of(More)
Traditional algorithms for the structure determination of native proteins by solution nuclear magnetic resonance (NMR) spectroscopy require a large number of experimental restraints. These algorithms formulate the structure determination problem as the computation of a structure or a set of similar structures that best fit the restraints. However, for both(More)
We present a novel structure determination approach that exploits the global orientational restraints from RDCs to resolve ambiguous NOE assignments. Unlike traditional approaches that bootstrap the initial fold from ambiguous NOE assignments, we start by using RDCs to compute accurate secondary structure element (SSE) backbones at the beginning of(More)
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,(More)
Since the first successful demonstration of the tunable alignment of ubiquitin in an anisotropic liquid crystal medium only eight years ago, much progress has been made in both NMR pulse techniques for the measurements of various residual dipolar couplings (RDCs) in both proteins and nucleic acids, and applications of RDCs to many important problems in(More)
The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering(More)