ArticleJournal of biomolecular NMR2008
Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm.
Article in Journal of biomolecular NMR, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Protonated Structure of EmrE Reveals C-terminal Tail Gating Mechanism.bioRxiv : the preprint server for biology · 2026Article
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- Automated fibril structure calculations in Xplor-NIH.Structure (London, England : 1993) · 2025Article
- Xplor-NIH: Better parameters and protocols for NMR protein structure determination.Protein science : a publication of the Protein Society · 2024Article
- Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue.Nature communications · 2024Article
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- Xplor-NIH for molecular structure determination from NMR and other data sources.Protein science : a publication of the Protein Society · 2018Article
- Creatine CEST MRI for Differentiating Gliomas with Different Degrees of Aggressiveness.Molecular imaging and biology · 2017Article
- The membrane localization domains of two distinct bacterial toxins form a 4-helix-bundle in solution.Protein science : a publication of the Protein Society · 2017Article
- NMRFAM-SDF: a protein structure determination framework.Journal of biomolecular NMR · 2015Article
- CEST signal at 2ppm (CEST@2ppm) from Z-spectral fitting correlates with creatine distribution in brain tumor.NMR in biomedicine · 2015Article
- Prefusion structure of syntaxin-1A suggests pathway for folding into neuronal trans-SNARE complex fusion intermediate.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data.Journal of biomolecular NMR · 2011Article
- Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.Methods in enzymology · 2011Article
- Solution structure of the 128 kDa enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide-angle X-ray scattering.Journal of the American Chemical Society · 2010Article
- Automated protein structure calculation from NMR data.Journal of biomolecular NMR · 2009Article
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4 authors.
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Abstract
We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258-6273). The improved protocol includes extensive analysis of input spectral data to create a low-resolution contact map of residues expected to be close in space. This map is used to obtain reasonable initial guesses of NOE assignment likelihoods which are refined during subsequent structure calculations. Information in the contact map about which residues are predicted to not be close in space is applied via conservative repulsive distance restraints which are used in early phases of the structure calculations. In comparison with the previous protocol, the new protocol requires significantly less computation time. We show results of running the new PASD protocol on six proteins and demonstrate that useful assignment and structural information is extracted on proteins of more than 220 residues. We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined.
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