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.

Shiftcor 1.3 – Compares, Identifies, Corrects and Re-referencs Protein Chemical Shifts

Shiftcor 1.3

:: DESCRIPTION

Shiftcor compares, identifies, corrects and re-referencs 1H, 13C and 15N backbone chemical shifts of peptides and proteins by comparing the observed chemical shifts with the predicted chemical shifts derived from the 3D structure (PDB corrdinates) of the protein(s)of interest.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Haiyan Zhang, Stephen Neal and David Wishart (2003)
“RefDB: A database of uniformly referenced protein chemical shifts”
Journal of Biomolecular NMR, 25: 173-195

PACSY / PACSY Maker b032814 / PACSY Analyzer – Database Management system for Protein Structure and Chemical Shift analysis

PACSY / PACSY Maker b032814 / PACSY Analyzer

:: DESCRIPTION

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Database Bank (PDB), the Biological Magnetic Resonance Data Bank (BMRB), and the Structural Classification of Proteins (SCOP) database.

PACSY Maker is used for building the PACSY database.

PACSY Analyzer is designed to provide an easy graphical user interface (GUI) for using PACSY database.

::DEVELOPER

The National Magnetic Resonance Facility at Madison (NMRFAM)

:: SCREENSHOTS

:: REQUIREMENTS

Linux

:: DOWNLOAD

PACSY, PACSY Maker , PACSY Analyzer

:: MORE INFORMATION

Citation

J Biomol NMR. 2012 Oct;54(2):169-79. Epub 2012 Aug 19.
PACSY, a relational database management system for protein structure and chemical shift analysis.
Lee W1, Yu W, Kim S, Chang I, Lee W, Markley JL.

CH3Shift – Structure Based Prediction of Protein Methyl Group Chemical Shifts

CH3Shift

:: DESCRIPTION

CH3Shift (CH3/methyl chemical shift predictor) is a method of calculating side-chain methyl chemical shifts from protein structures

::DEVELOPER

Aleksandr Sahakyan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
R

:: DOWNLOAD

CH3Shift

:: MORE INFORMATION

Citation

J Biomol NMR. 2011 Aug;50(4):331-46. doi: 10.1007/s10858-011-9524-2. Epub 2011 Jul 12.
Structure-based prediction of methyl chemical shifts in proteins.
Sahakyan AB1, Vranken WF, Cavalli A, Vendruscolo M.

SHIFTX2 1.13 – Improved Protein Chemical Shift Prediction

SHIFTX2 1.13

:: DESCRIPTION

SHIFTX2 is a web server that predicts 1H, 13C, and 15N protein chemical shifts using the 3D structure (PDB coordinates) of the protein of interest for both backbone and sidechain atoms.SHIFTX2 combines ensemble machine learning methods with sequence alignment-based methods to calculate protein chemical shifts for backbone and side chain atoms. SHIFTX2 has been trained on a carefully selected set of 197 proteins and tested on a separate set of 61 proteins. Both the training and testing sets consisted of high resolution X-ray structures (<2.1 Angs) with carefully verified chemical shifts assignments. SHIFTX2 is able to attain correlation coefficients between experimentally observed and predicted backbone chemical shifts of 0.9800 (15N), 0.9959 (13CA), 0.9992 (13CB), 0.9676 (13CO), 0.9714 (1HN), 0.9744 (1HA) and RMS errors of 1.1169, 0.4412, 0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. Comparisons to other chemical shift predictors using the same testing data set indicates that SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3X smaller) than any other program.

::DEVELOPER

Wishart Pharmaceutical Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX
Python
GCC/G++ Compiler
Java

:: DOWNLOAD

SHIFTX2

:: MORE INFORMATION

Citation

Beomsoo Han, Yifeng Liu, Simon Ginzinger, and David Wishart. (2011)
SHIFTX2: significantly improved protein chemical shift prediction.
Journal of Biomolecular NMR, Volume 50, Number 1, 43-57. doi: 10.1007/s10858-011-9478-4

GeNMR – Webserver for Protein Structure generation from NOE Distant Restraints and Chemical Shifts

GeNMR

:: DESCRIPTION

GeNMR (GEnerate NMR structure) is a web server for generating 3D protein structures using NOE-derived distance restraints and NMR chemical shifts.

::DEVELOPER

GeNMR team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W670-7. doi: 10.1093/nar/gkp280. Epub 2009 Apr 30.
GeNMR: a web server for rapid NMR-based protein structure determination.
Berjanskii M1, Tang P, Liang J, Cruz JA, Zhou J, Zhou Y, Bassett E, MacDonell C, Lu P, Lin G, Wishart DS.

SHIFTS 5.5 – Predict Nitrogen, Carbon & Proton Chemical Shifts in Proteins

SHIFTS 5.5

:: DESCRIPTION

SHIFTS takes a protein structure in Brookhaven (PDB) format, and computes proton chemical shifts from empirical formulas. It can also compute N, C`alpha`, C`beta` and C’ shifts in proteins, using a database based on DFT calculations on peptides.

Shifts Web Version

::DEVELOPER

the Case group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Window with Cygwin / Linux / Mac OsX
NAB

:: DOWNLOAD

SHIFTS

:: MORE INFORMATION

Citation

X.P. Xu and D.A. Case.
Probing multiple effects on ¹⁵N, ¹³Ca, ¹³Cb and ¹³C’ chemical shifts in peptides using density functional theory.
Biopolymers 65 408-423 (2002).

acACS 1.0 – Auto Covariance of Average Chemical Shifts

acACS 1.0

:: DESCRIPTION

acACS is a web-servers for generating auto covariance of average chemical shifts from native amino acids and second structure.

::DEVELOPER

The Li’s Group of Theoretical Biophysics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Borowser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Guo-liang Fan and Qianzhong Li,
Predicting protein submitochondria locations by combining different descriptors into the general form of Chou’s pseudo amino acid composition,
Amino Acids, 43 (2012) 545–555.

Guoliang Fan and Qianzhong Li,
Predict mycobacterial proteins subcellular locations by incorporating pseudo-average chemical shift into the general form of Chou’s pseudo amino acid composition,
Journal of Theoretical Biology, 304 (2012) 88–95.

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

:: 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

:: 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.