Evidence map›Paper›PMID 25900069›Full record

ArticleJournal of biomolecular NMR2015

NMRFAM-SDF: a protein structure determination framework.

Hesam Dashti, Woonghee Lee, Marco Tonelli, Claudia C Cornilescu, Gabriel Cornilescu, Fariba M Assadi-Porter, William M Westler, Hamid R Eghbalnia, John L Markley

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of biomolecular NMR, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Integrative NMR for biomolecular research.Journal of biomolecular NMR · 2016
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Hesam DashtiNational Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
Woonghee LeeNational Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
Marco TonelliNational Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
Claudia C CornilescuNational Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
Gabriel CornilescuNational Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
Fariba M Assadi-PorterNational Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
William M WestlerNational Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
Hamid R EghbalniaNational Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
John L MarkleyNational Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA. markley@nmrfam.wisc.edu.

Funding

TR&D 3: TECHNOLOGY DEVELOPMENT FOR NMR STUDIES OF SMALL MOLECULES (METABOLOMICS, NATURAL PRODUCTS, METABOLITE-PROTEIN INTERACTIONS) pp.537-585 P41GM103399 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI BUTCHER, SAMUEL E · 2012 to 2019
$9.4M
Integrated state-of-the-art LC-MS/NMR system for the University of WisconsinS10RR025062 · NCRR · UNIVERSITY OF WISCONSIN-MADISON · PI MARKLEY, JOHN LUTE · 2008 to 2008
$1.7M
Upgrade of the NMRFAM 750 MHz NMR SpectrometerS10RR029220 · NCRR · UNIVERSITY OF WISCONSIN-MADISON · PI MARKLEY, JOHN LUTE · 2010 to 2010
$766k
NMR Spectrometer System Optimized for Direct 13C or 15N DetectionS10RR023438 · NCRR · UNIVERSITY OF WISCONSIN-MADISON · PI MARKLEY, JOHN LUTE · 2008 to 2008
$500k
WIDE-BORE 9.4 TESLA NMR SPECTROMETER FOR UW-MADISONS10RR002781 · NCRR · UNIVERSITY OF WISCONSIN MADISON · PI MARKLEY, JOHN L · 1986 to 1986
–
CONSOLE UPGRADES FOR NMR FACILITYS10RR008438 · NCRR · UNIVERSITY OF WISCONSIN MADISON · PI MARKLEY, JOHN L · 1993 to 1993
–
NCRR NIH HHS S10 RR002781NCRR NIH HHS S10 RR008438NCRR NIH HHS S10 RR023438NCRR NIH HHS S10RR023438NCRR NIH HHS S10 RR025062NCRR NIH HHS S10RR025062NCRR NIH HHS S10 RR029220NCRR NIH HHS S10RR029220NIGMS NIH HHS P41 GM103399NIGMS NIH HHS P41GM103399
6 · The paper itself

Abstract

The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR--from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm).

Indexed as

Nuclear Magnetic Resonance, BiomolecularSoftwareCarbon-13 Magnetic Resonance SpectroscopyModels, MolecularProtein ConformationProteinsWeb BrowserWorkflowProteinsADAPT-NMRARECAAutomated protein structure determination frameworkCASD-NMRNon-uniform samplingPINEPONDEROSA-C/SValidation

Identifiers

PMID25900069
PMCPMC4569665

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.