Tag: NMR

LACS – Validate Protein NMR Chemical Shifts

LACS

:: DESCRIPTION

LACS ( linear analysis of chemical shifts) is a validation tool for protein backbone NMR chemical shift data. Based on the observation that secondary chemical shift (difference between the chemical shift of an amino acid and its random coil chemical shift) well indicate the local backbone geometry, LACS correlates the secondary chemical shifts of a nucleus to that of Ca-Cb of itself (referencing independent), thus avoiding any geometry or structure assumptions, to estimate referencing offsets and identify possible miss-assignments.

::DEVELOPER

Liya Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 LACS

:: MORE INFORMATION

Citation

Wang, L.; Eghbalnia, H. R.; Bahrami, A.; Markley, J. L.,
Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications,
J. Biomol. NMR 25, 32, 13-22.

RDC-PANDA 1.0 – NMR NOE Assignment & Protein Structure Determination

RDC-PANDA 1.0

:: DESCRIPTION

RDC-PANDA (RDC-based SSE PAcking with NOEs for Structure Determination and NOE Assignment) is a suite of programs for nuclear Overhauser effect (NOE) assignment and high-resolution structure determination starting with a global fold calculated from exact solutions to the residual dipolar coupling (RDC) equations. RDC-PANDA is specifically designed for automated NMR NOE assignment and protein structure determination.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

RDC-PANDA

:: MORE INFORMATION

Citation

Jianyang Zeng, Jeffrey Boyles, Chittaranjan Tripathy, Lincong Wang, Anthony Yan, Pei Zhou, and Bruce Randall Donald.
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.
Journal of Biomolecular NMR, 45(3):265-281, 2009

Peakr – Simulating 2D Solid-state NMR Spectra

Peakr

:: DESCRIPTION

Peakr is a software to simulate solid-state NMR spectra of proteins.

::DEVELOPER

Peakr team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 1;29(9):1134-40. doi: 10.1093/bioinformatics/btt125. Epub 2013 Mar 14.
Peakr: simulating solid-state NMR spectra of proteins.
Schneider R1, Odronitz F, Hammesfahr B, Hellkamp M, Kollmar M.

Vivaldi – Visualisation, Analysis and Validation of NMR entries

Vivaldi

:: DESCRIPTION

Vivaldi is a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB).

::DEVELOPER

Protein Data Bank in Europe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.
Hendrickx PM, Gutmanas A, Kleywegt GJ.
Proteins. 2013 Apr;81(4):583-91. doi: 10.1002/prot.24213

Mobi 1.1 – NMR Mobility Detection

Mobi 1.1

:: DESCRIPTION

Mobi is a new web server to detect and visualize flexible regions in NMR solved structures. Mobi is based on a simple algorithm to find regions with different conformations among all the models in a NMR solved PDB structure ensemble.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Nov 15;26(22):2916-7. doi: 10.1093/bioinformatics/btq537. Epub 2010 Sep 21.
MOBI: a web server to define and visualize structural mobility in NMR protein ensembles.
Martin AJ1, Walsh I, Tosatto SC.

PREDITOR – Predicting Torsion Angles in Proteins from NMR Chemical Shifts and/or Homology

PREDITOR

:: DESCRIPTION

PREDITOR is a program for PREDIcting φ, ψ, χ1, and ω TORsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology. PREDITOR 30o-accuracy of predicting φ and ψ is close to 90%. The average χ1 accuracy is 84% while the ω accuracy is 99.98% for trans peptide bond identification and 93% for cis peptide bond identification.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

PREDITOR: a web server for predicting protein torsion angle restraints.
Berjanskii MV, Neal S, Wishart DS.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W63-9.

SHIFTOR – Predicting Torsion Angles in Proteins from NMR Chemical Shifts and Sequence Homology

SHIFTOR

:: DESCRIPTION

SHIFTOR is a program for predicting φ, ψ, χ1, and ω torsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Magn Reson Chem. 2006 Jul;44 Spec No:S158-67.
Accurate prediction of protein torsion angles using chemical shifts and sequence homology.
Neal S, Berjanskii M, Zhang H, Wishart DS.

CS23D 2.0 – Protein Structure generation using NMR Chemical Shifts and Sequence data

CS23D 2.0

:: DESCRIPTION

CS23D (Chemical Shift to 3D Structure) is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W496-502. doi: 10.1093/nar/gkn305. Epub 2008 May 30.
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data.
Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G.

ResProx – Comparing the overall Quality of NMR Protein Structures

ResProx

:: DESCRIPTION

ResProx (Resolution-by-proxy or Res(p)) is a web server that predicts the atomic resolution of NMR protein structures using only PDB coordinate data as input.

::DEVELOPER

Wishart Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • VMware

:: DOWNLOAD

  ResProx

:: MORE INFORMATION

Citation

Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
Berjanskii M, Zhou J, Liang Y, Lin G, Wishart DS.
J Biomol NMR. 2012 Jul;53(3):167-80. doi: 10.1007/s10858-012-9637-2

GSC 1.2 – NMR Chemical Shift Comparison

GSC 1.2

:: DESCRIPTION

GSC is a tcl/tk program which makes it easy to analyze chemical shifts of selected atoms between chemical shift files

::DEVELOPER

Brian Sykes Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GSC

:: MORE INFORMATION

Citation

Wolfram Gronwald , R. Boyko, and B.D. Sykes.
GSC: a graphical program for NMR chemical shifts comparison
Comput Appl Biosci (1997) 13 (5): 557-558

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