Software Development Brian Sykes Lab

1. atom_comp Atom comparison and energy calculations for an ensemble pdb file.

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. nic 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 required functionality.

5. nmrtools - nmr scripts that we find useful in the lab, currently includes modfid and various vnmrj macros and scripts.

6. 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.

7. orbplus 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.

8. 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 .

9. ppscan 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 experiments.

10. 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.

11. 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.

12. 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.

13. 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.

14. 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.

15. 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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