Brian Sykes Lab
atom_comp Atom comparison and energy calculations for an ensemble
csi which stands for chemical shift index
is a program for the identification of protein secondary structure
using 13-C chemical shift data .
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.
which stands for NMR Integration calculations is software developed
to integrate a series of spectral data files.
Our data was obtained on the fluorimeter, however any two column coordinate
data input is all that is required. The impetus for this software arises
from the lack of our spreadsheet programs to provide the
- nmr scripts that we find useful in the lab, currently includes
modfid and various vnmrj macros and scripts.
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.
Structural Feature Prediction Tool - This software summarizes and predicts the properties of an input protein
using only the assigned chemical shift information of a target protein.
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
extract parameter values from a vnmrj procpar file for all the fids
located in a directory.
Output the resulting table to be read and analyzed with Excel. We use this
script in our lab to see how shims have changed for various related vnmrj
is a comprehensize protein sequence analysis package
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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