ArticleBioinformatics (Oxford, England)2018
PINE-SPARKY.2 for automated NMR-based protein structure research.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Modernizing biomolecular NMR: The POKY suite.The Journal of biological chemistry · 2026Review
- Article
- A Novel Mechanism of Coactivator Recruitment by the Nurr1 Nuclear Receptor.Journal of molecular biology · 2022Article
- ssPINE: Probabilistic Algorithm for Automated Chemical Shift Assignment of Solid-State NMR Data from Complex Protein Systems.Membranes · 2022Article
- Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach.Protein science : a publication of the Protein Society · 2022Article
- Backbone and sidechainBiomolecular NMR assignments · 2022Article
- POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data.Journal of structural biology: X · 2022Article
- Toho-1 β-lactamase: backbone chemical shift assignments and changes in dynamics upon binding with avibactam.Journal of biomolecular NMR · 2021Article
- CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery.Bioinformatics (Oxford, England) · 2021Article
- Solution structures of the Shewanella woodyi H-NOX protein in the presence and absence of soluble guanylyl cyclase stimulator IWP-051.Protein science : a publication of the Protein Society · 2021Article
- Article
- Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase α-subunit from solution-state NMR.Journal of biomolecular NMR · 2020Article
- Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum.Nature communications · 2019Article
- Backbone resonance assignments and secondary structure of Ebola nucleoprotein 600-739 construct.Biomolecular NMR assignments · 2019Article
- Article
- Applications of In-Cell NMR in Structural Biology and Drug Discovery.International journal of molecular sciences · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Summary: Nuclear magnetic resonance (NMR) spectroscopy, along with X-ray crystallography and cryoelectron microscopy, is one of the three major tools that enable the determination of atomic-level structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein-ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. The graphical user interface of PINE-SPARKY.2 simplifies chemical shift assignment and verification, automated detection of secondary structural elements, predictions of flexibility and hydrophobic cores, and calculation of three-dimensional structural models. Availability and implementation: PINE-SPARKY.2 is available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers to the SBGrid (https://sbgrid.org). For a detailed description of the program, see http://www.nmrfam.wisc.edu/pine-sparky2.htm. Contact: whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.