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NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Unread 10-03-2005, 11:09 PM
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Below is a copy of Software Development web.page of Bryan Sykes's lab







[b]
Software Development

Brian Sykes Lab





  1. csi
    which stands for chemical shift index
    is a program for the identification of protein secondary structure
    using 13-C chemical shift data
    .





  2. 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.





  3. 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.





  4. 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 .





  5. 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.





  6. 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.





  7. 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.





  8. 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.





  9. 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.





  10. 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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