csi which stands for chemical shift index
is a program for the identification of protein secondary structure
using 13-C chemical shift data .
gsc analyzes and compares chemical shift files on a graphical basis.
If you have two or more sequences and want to see the chemical shift
similarity, this is a nice way to do it.
orb predicts chemical shifts based on homologous proteins employing a
graphical user interface.
Orb thoughtfully considers global sequence homology, local sequence homology,
structural homology, and molecular homology in determining its predictions.
which stands for Pure Java NMR is an NMR pulse sequence simulation
tool modelled after MacNMR. It includes functionality for gradients.
The old MacNMR (for classic environments only) is available here .
is a comprehensize protein sequence analysis package
commercialized by biotools.
SEQSEE (SEQuence SEEr) is a multi-purpose menu-driven suite of
programs designed to provide a fully integrated analysis of protein
sequences and protein databases. It contains rapid database searching,
flexible pattern matching and multiple sequence alignment as well
as a large number of structural analysis and prediction programs.
is an intuitive semi-automated nmr assignment tool . Currently
configured for graphics display within
it displays the potential basic
sequential connectivities in spectra, allows chaining of
these connectivities for assignment, and keeps track of bookkeeping issues
involving chainlists, peaklists and chemical shift files.
which stands for structural thermodynamic calculations
performs free energy calculations from the structure of
the different complexes within a graphical user interface.
First, stc calculates the change in accessible surface area (ASA) for the
dissociation process from the coordinate pdb files. It then
calculates the energetics from the change in ASA.
performs structural analysis of protein coordinate data .
It provides the user with objective information on secondary structure,
residue volume, accessible surface area as well as phi and psi angles,
and hbonds. This data is further collated to provide a summary information
and a quality index.
is a tool for multiple sequence alignment based on sequence homology and
The user has the ability to include specific insights or knowledge into the
alignment through sequence anchoring, clustering, changing the amino acid
similarity matrix, gapping penalties, or even the order in which the
sequences are aligned.
performs binding curve studies and curve fitting for NMR
spectroscopic analysis .
Functions include T1/T2 relaxation, gaussian, pH titration, etc, and the output
includes postscript plots, the rmse of fit, a measure of the sensitivity of
each fitting function parameter, and a table showing how each datapoint
fits the function.
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A source of RPMs for several NMR-related programs
BioLinux-BR Project offers RPM packages for such popular programs as MolMol, PROCHECK and XPLOR-NIH.
Project description from its website:
BioLinux-BR is a project directed to the scientific community. Our intention is to create a Linux distribution for people with little familiarity with the installation of the operational system and mainly for people that do not know how they must proceed to unpack a program, compile and install it correctly.
For these reasons, we are giving our contribution, developing a Linux system that aims to be easy to use and still offering packages that...
12-18-2014 09:29 AM
[NMR900 blog] Recognition: Brian Sykes
Recognition: Brian Sykes
Brian Sykes, a Distinguished University Professor in the Department of Biochemistry, University of Alberta, has won the 2010 University of Alberta Cup. The University Cup is among the highest honors that the University of Alberta confers on its faculty members. It is awarded in recognition of faculty members who have clearly excelled in both teaching and research. Prof. Sykes was presented with the University Cup at the 2011 Celebrate! ceremony, the university’s annual celebration of teaching, learning and research, held on September 16, 2011 (read the news...
News from NMR blogs
10-09-2011 06:15 AM
[NMR paper] Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignme
Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments.
Related Articles Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments.
J Biomol NMR. 2003 Dec;27(4):313-21
Authors: Slupsky CM, Boyko RF, Booth VK, Sykes BD
Complete and accurate NMR spectral assignment is a prerequisite for high-throughput automated structure determination of biological macromolecules. However, completely automated assignment procedures generally encounter difficulties for all but the most ideal data...
11-24-2010 09:16 PM
[Question from NMRWiki Q&A forum] What does ph2:r statement do in Bruker pulse programs
What does ph2:r statement do in Bruker pulse programs
Found a following statement in the pulse program called selnogp
p12:sp2:f1 ph2:r What does this do - specifically last bit of the second part - ph2:r the :r?
The first one - I understand shaped pulse at power sp2, shape spnam2 and length p12.
Looks like ph2 is the phase for the shaped pulse - is that right?
Programs for alignment of protein NMR ensembles
If you need to align models in your NMR ensemble, you can use the following programs to do so. MolMol
- Official website
- Linux binaries from Patrick Finerty website
- BioXRay distribution
Bruker pulse programs
Ad Bax's pulse sequence library
Ad Bax's note: This library contains recently published pulse sequences that have been tested on our equipment. By downloading, viewing or using any of them you acknowledge our rules as outlined in disclaimer and copyright.
Bruker pulse sequences from Gordon Rule
Gordon Rule note: ALL of these employ gradients for artifact suppression. None are sensitivity enhanced. In all HN experiments the water is suppressed by a watergate-type sequence. In some cases crusher gradients are also used. These sequences have been...