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PACSY specifications

Information


Unique identifier OMICS_06814
Name PACSY
Alternative name Protein structure And Chemical Shift NMR spectroscopy
Restrictions to use None
Maintained Yes

Publication for Protein structure And Chemical Shift NMR spectroscopy

PACSY citations

 (3)
call_split

PINE SPARKY.2 for automated NMR based protein structure research

2017
Bioinformatics
PMCID: 5925765
PMID: 29281006
DOI: 10.1093/bioinformatics/btx785
call_split See protocol

[…] ; (iii) visualize PINE probabilities for spin system assignments (); (iv) visualize chemical shift referencing analysis by the LACS algorithm ();(v) visualize hydrophobic core residues predicted from PACSY database (; ); (vi) visualize RCI S2 (random coil index order parameter; ); and/or (vii) generate PINE probabilistic labels and accept the most probable ones with P > 0.5 (). Then the Completene […]

library_books

The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

2016
J Biomol NMR
PMCID: 4921114
PMID: 27169728
DOI: 10.1007/s10858-016-0036-y

[…] ds upper limits with elastic settings. By default, calculations are run on the NMRFAM-hosted Ponderosa Server. Users can run the software on their own hardware by installing the Ponderosa Server, the PACSY database, and the PACSY PDBSEQ_DB table expansion as described in Supplementary Table S1. AUDANA also can be launched directly from NMRFAM-SPARKY (Lee et al. ) by invoking “Calculation of 3D str […]

call_split

Integrative NMR for biomolecular research

2016
J Biomol NMR
PMCID: 4861749
PMID: 27023095
DOI: 10.1007/s10858-016-0029-x
call_split See protocol

[…] erosa Server, and the NOESY peak picking and data transfer program on the client side, Ponderosa Client, are written in C++ with QT libraries (http://www.qt.io). We developed an interface between the PACSY database and Ponderosa Server to support the AUDANA algorithm (Automated Database-Assisted NOESY Assignment) for automated structure calculation (Lee et al., submitted) and the PACSY-ALIGN algor […]

Citations

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PACSY institution(s)
National Magnetics Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA

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