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PALES specifications

Information


Unique identifier OMICS_19956
Name PALES
Alternative name Prediction of ALignmEnt from Structure
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A 3D structure with protons.
Input format PDB
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 10.4.8
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Markus Zweckstetter <>

Publications for Prediction of ALignmEnt from Structure

PALES in publications

 (17)
PMCID: 5827114
PMID: 29483512
DOI: 10.1038/s41467-018-03182-3

[…] different tensor values for the nurr-domain (d −17.7 and r 0.22) and the extrrm1 domain (d −18.0 and r 0.31) as obtained from the best fit of the rdc data to the crystal structure with the program pales. two-hundred structures were calculated that grouped into three clusters (clusters 1,2,3 having 106, 68, 21 structures respectively) representing 97.5% of the structures. cluster 1 is by far […]

PMCID: 5861439
PMID: 29300933
DOI: 10.1093/nar/gkx1283

[…] using ccpnmr analysis (). the magnitude (da) and rhombicity (r) of the alignment tensor were derived by fitting the experimental rdcs to pdb 1roc using singular-value decomposition as implemented in pales (). csps were calculated as \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} […]

PMCID: 5435913
PMID: 28369571
DOI: 10.1093/nar/gkx186

[…] a monte carlo sampling scheme was used to search for the ensemble that minimizes the differences between the measured rdcs and values back-calculated for a given trial ensemble using the program pales (). we have previously validated the use of pales in the generation of nucleic acid ensembles (). the initial effective temperature used in the monte carlo scheme was set to 1 k and decreased […]

PMCID: 5279813
PMID: 28085875
DOI: 10.1371/journal.pcbi.1005314

[…] backbones with respect to external magnetic field, and can identify long-range structural correlations across biomolecular structure. to compute rdc constants from in silico structures we used the prediction of alignment from structure (pales) program []. we processed our simulation structures by using default pales settings, including the application of steric interaction model, […]

PMCID: 4838374
PMID: 26883628
DOI: 10.1093/nar/gkw084

[…] dinter(h2′i-h6/8i+1), dinter(h2″i-h6/8i+1) were directly inferred from the added protons. rdcs involving c6/8-h6/8, c3′-h3′, c4′-h4′ vectors were calculated on x-ray structures with pales (), using a concentration of pf1 phage of 10 mg/ml., in addition to the x-ray structures, a series of dna models were generated with 3dna (). they are based on canonical b-dna structures […]


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PALES institution(s)
Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
PALES funding source(s)
Supported by the Max Planck Society and the DFG through grants ZW71/1-1 to 3-1.

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