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Protocols

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

Versioning


No version available

Maintainer


  • person_outline Markus Zweckstetter

Publications for Prediction of ALignmEnt from Structure

PALES citations

 (34)
library_books

A cryptic RNA binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets

2018
Nat Commun
PMCID: 5827114
PMID: 29483512
DOI: 10.1038/s41467-018-03182-3

[…] th 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 the […]

library_books

Structural characterization of the Asf1–Rtt109 interaction and its role in histone acetylation

2017
Nucleic Acids Res
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 or . […]

library_books

Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three dimensional Structure Determination of Proteins Open Avenues for Life Scientists

2017
Comput Struct Biotechnol J
PMCID: 5408130
PMID: 28487762
DOI: 10.1016/j.csbj.2017.04.001

[…] nt of alignment of the protein.From the Cartesian coordinates of the aligned protein, it is theoretically possible to predict the alignment tensor of the weakly aligned protein using programs such as PALES or REDCAT by simulation of the predicted dipolar coupling between the bond vector and the principal axes of the estimated alignment tensor of the protein.RDC values can also be calculated from […]

library_books

Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

2017
Nucleic Acids Res
PMCID: 5435913
PMID: 28369571
DOI: 10.1093/nar/gkx186

[…] ata. 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 by […]

call_split

Is the Conformational Ensemble of Alzheimer’s Aβ10 40 Peptide Force Field Dependent?

2017
PLoS Comput Biol
PMCID: 5279813
PMID: 28085875
DOI: 10.1371/journal.pcbi.1005314
call_split See protocol

[…] in 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, which determin […]

library_books

The intrinsic mechanics of B DNA in solution characterized by NMR

2016
Nucleic Acids Res
PMCID: 4838374
PMID: 26883628
DOI: 10.1093/nar/gkw084

[…] r(H6/8i-H6/8i+1), 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 (called ‘ […]


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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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