Evidence map›Paper›PMID 25515756›Full record

ArticleBioinformatics (Oxford, England)2015

LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins.

Darui Xu, Kara Marquis, Jimin Pei, Szu-Chin Fu, Tolga Cağatay, Nick V Grishin, Yuh Min Chook

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.

0numbers the graph read from it
0cells of the map it votes in
102citing papers in PubMed
3.3field-weighted citation impact, top 7% of its field
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

102 citing papers in PubMed, 185 citations in OpenAlex.

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42 more citing papers are in PubMed but not listed here.

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

7 authors at 1 institution in 1 country.

Darui XuDepartment of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.
Kara MarquisDepartment of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.
Jimin PeiDepartment of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.
Szu-Chin FuDepartment of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.
Tolga CağatayDepartment of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.
Nick V GrishinDepartment of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.
Yuh Min ChookDepartment of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA, Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050, USA.
The University of Texas Southwestern Medical Center · US

Funding

Structures and Mechanisms of Nuclear Import and ExportR01GM069909 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI CHOOK, YUH MIN · 2004 to 2020
$5.8M
Computational methods for structural-functional studies of proteinsR01GM094575 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI GRISHIN, NICK V. · 2010 to 2017
$2.4M
Database and Prediction Algorithm for the Leucine-rich Nuclear Export SignalsF32GM093493 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI XU, DARUI · 2010 to 2011
$99k
Howard Hughes Medical InstituteNIGMS NIH HHS F32GM093493NIGMS NIH HHS GM094575NIGMS NIH HHS R01 GM069909
6 · The paper itself

Abstract

motivationClassical nuclear export signals (NESs) are short cognate peptides that direct proteins out of the nucleus via the CRM1-mediated export pathway. CRM1 regulates the localization of hundreds of macromolecules involved in various cellular functions and diseases. Due to the diverse and complex nature of NESs, reliable prediction of the signal remains a challenge despite several attempts made in the last decade.

resultsWe present a new NES predictor, LocNES. LocNES scans query proteins for NES consensus-fitting peptides and assigns these peptides probability scores using Support Vector Machine model, whose feature set includes amino acid sequence, disorder propensity, and the rank of position-specific scoring matrix score. LocNES demonstrates both higher sensitivity and precision over existing NES prediction tools upon comparative analysis using experimentally identified NESs. AVAILABILITY AND IMPLEMENTATION: LocNES is freely available at http://prodata.swmed.edu/LocNES CONTACT: yuhmin.chook@utsouthwestern.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

Nuclear Export SignalsSoftwareAmino Acid SequenceConsensus SequenceExportin 1 ProteinHumansKaryopherinsPosition-Specific Scoring MatricesReceptors, Cytoplasmic and NuclearSequence Analysis, ProteinSupport Vector MachineExportin 1 ProteinKaryopherinsNuclear Export SignalsReceptors, Cytoplasmic and Nuclear

Identifiers

PMID25515756
PMCPMC4410651
OpenAlexW2155917943

What OpenQuestion holds

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Registered trials

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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.