Bryan Sykes's lab NMR programs: csi, gsc, orb, pjnmr, smartnotebook, etc.

[nmrlearner]

Below is a copy of Software Development web.page of Bryan Sykes's lab

[b] Software Development Brian Sykes Lab

2. 
   
   csi which stands for chemical shift index
   is a program for the identification of protein secondary structure
   using 13-C chemical shift data .
   
   
   
   
3. 
   
   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.
   
   
   
   
4. 
   
   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.
   
   
   
   
5. 
   
   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 .
   
   
   
   
6. 
   
   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.
   
   
7. 
   
   
   
   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.
   
   
   
   
8. 
   
   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.
   
   
   
   
9. 
   
   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.
   
   
   
   
10. 
    
    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.
    
    
    
    
11. 
    
    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.