10-03-2005, 11:09 PM
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Senior Member
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Join Date: Jan 2005
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Below is a copy of Software Development web.page of Bryan Sykes's lab
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[b]
Software Development
Brian Sykes Lab
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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.
pjnmr
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 .
seqsee
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.
smartnotebook
is an intuitive semi-automated nmr assignment tool . Currently
configured for graphics display within
nmrview,
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.
stc
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.
vadar
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.
xalign
is a tool for multiple sequence alignment based on sequence homology and
secondary structure.
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.
xcrvfit
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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