ArticleJournal of biomolecular NMR2006
PASA--a program for automated protein NMR backbone signal assignment by pattern-filtering approach.
Article in Journal of biomolecular NMR, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
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- Gene duplications facilitate C4-CAM compatibility in common purslane.Plant physiology · 2023Article
- Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome.Nature plants · 2021Article
- Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild.Evolution letters · 2020Article
- Structural Basis of Paxillin Recruitment by Kindlin-2 in Regulating Cell Adhesion.Structure (London, England : 1993) · 2019Article
- Structure of Rap1b bound to talin reveals a pathway for triggering integrin activation.Nature communications · 2017Article
- The draft genome sequence of a desert tree Populus pruinosa.GigaScience · 2017Article
- NMRFAM-SDF: a protein structure determination framework.Journal of biomolecular NMR · 2015Article
- Exploiting image registration for automated resonance assignment in NMR.Journal of biomolecular NMR · 2015Article
- Structural mechanism of integrin inactivation by filamin.Nature structural & molecular biology · 2015Article
- The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.Nature communications · 2014Article
- TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra.Journal of biomolecular NMR · 2012Article
- Membrane binding of the N-terminal ubiquitin-like domain of kindlin-2 is crucial for its regulation of integrin activation.Structure (London, England : 1993) · 2011Article
- RDC derived protein backbone resonance assignment using fragment assembly.Journal of biomolecular NMR · 2011Article
- Generalized indirect covariance NMR formalism for establishment of multidimensional spin correlations.The journal of physical chemistry. A · 2009Article
- Migfilin, a molecular switch in regulation of integrin activation.The Journal of biological chemistry · 2009Article
- Automated structure determination from NMR spectra.European biophysics journal : EBJ · 2009Review
- Graphical interpretation of Boolean operators for protein NMR assignments.Journal of biomolecular NMR · 2008Article
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5 authors.
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Abstract
We present a new program, PASA (Program for Automated Sequential Assignment), for assigning protein backbone resonances based on multidimensional heteronuclear NMR data. Distinct from existing programs, PASA emphasizes a per-residue-based pattern-filtering approach during the initial stage of the automated 13Calpha and/or 13Cbeta chemical shift matching. The pattern filter employs one or multiple constraints such as 13Calpha/Cbeta chemical shift ranges for different amino acid types and side-chain spin systems, which helps to rule out, in a stepwise fashion, improbable assignments as resulted from resonance degeneracy or missing signals. Such stepwise filtering approach substantially minimizes early false linkage problems that often propagate, amplify, and ultimately cause complication or combinatorial explosion of the automation process. Our program (http://www.lerner.ccf.org/moleccard/qin/) was tested on four representative small-large sized proteins with various degrees of resonance degeneracy and missing signals, and we show that PASA achieved the assignments efficiently and rapidly that are fully consistent with those obtained by laborious manual protocols. The results demonstrate that PASA may be a valuable tool for NMR-based structural analyses, genomics, and proteomics.
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