Xplor-NIH statistics

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Xplor-NIH specifications

Information


Unique identifier OMICS_03403
Name Xplor-NIH
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format PDB
Operating system Unix/Linux
Programming languages C++, Python
Computer skills Advanced
Version 2.43
Stability Stable
Requirements
XPLOR
Maintained Yes

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Maintainer


  • person_outline Junji Iwahara <>

Publication for Xplor-NIH

Xplor-NIH in pipeline

2016
PMCID: 5017827
PMID: 27626070
DOI: 10.1126/sciadv.1501228

[…] 600 to 900 mhz using bruker spectrometers. nmr spectra were processed using topspin and nmrpipe () and analyzed using nmrview () and sparky ()., initial structure calculations were conducted within xplor-nih v2.24 () using rmd with simulated annealing. this led to an ensemble of kcne3 structures consistent with the nmr data. ten of the top-scoring 1% xplor-nih–generated kcne3 structures […]


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Xplor-NIH in publications

 (206)
PMCID: 5913134
PMID: 29686383
DOI: 10.1038/s41467-018-03886-6

[…] to ponderosa client (http://ponderosa.nmrfam.wisc.edu/), and ponderosa analyzer was used to interatively refine and validate the resulting structural ensemble. ponderosa uses cyana automation and xplor-nih–., docking simulations were performed using the protein docking prediction server cluspro (https://cluspro.bu.edu/home.php). cluspro can simulate protein docking of oligomer forms, […]

PMCID: 5902452
PMID: 29662055
DOI: 10.1038/s41467-018-03746-3

[…] each free induction decay. the experiment was acquired in an edited mode. all nmr data were processed using nmrpipe and analyzed with nmr view., the structure calculations were performed with the xplor-nih version 2.28 software by simulated annealing (sa) algorithm. noe intensities were converted into semi-quantitative distance restrains using the calibration by hyberts et al.. the angle […]

PMCID: 5897548
PMID: 29681894
DOI: 10.3389/fmicb.2018.00667

[…] respectively). forty-four dihedral angle restrains were obtained from analysis of cα, hα, cβ, n, and hn chemical shifts with the program talos+ (). structure calculations were performed using the xplor-nih software, version 2.27 (). a total of 100 structures, starting with an extended conformation, were generated using a simulated annealing protocol, followed by 20,000 steps of simulated […]

PMCID: 5908246
PMID: 29562181
DOI: 10.1016/j.celrep.2018.02.097

[…] the maximum csp of any residue within each defined hydrophobic cluster., the structure of freeform med15 abd2 (aa 277–368) was determined based on chemical shifts, noes, and n-h rdcs using the xplor-nih software () with the eefx implicit water potential (). noes were assigned manually and used as distance restraints. dihedral backbone restraints were calculated from backbone chemical […]

PMCID: 5832863
PMID: 29497118
DOI: 10.1038/s41598-018-22177-0

[…] and amino groups, which amounts to the 93.2% completeness of 1h assignment. three-dimensional 13c-separated noe and 15n-separated noe restraints were employed for the structure calculation using the xplor-nih program. residual dipolar couplings (rdcs) were measured in 10 mg/ml of pf1 phage alignment medium. the structure was determined using 1,782 nmr restraints including 1,504 experimental […]


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Xplor-NIH institution(s)
Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD, USA; Laboratory of Biophysical Chemistry, National Heart Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, USA; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA

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