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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 01-29-2013, 07:23 AM
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Default Are you interested in further development of PPT-DB: the protein property prediction and testing database?

If you find PPT-DB useful for your research or would like to suggest a new feature, you can let program developers know here.

PPT-DB info:

Quote:
PPT-DB is a database of protein property databases. PPT-DB can be used by both software developers and protein chemists. To use the database, click on any of the database links on the left margin. Users can download the databases, search by text or search by sequence. Learn more about the database by clicking the navigation buttons located at the top of this page.

Protein Chemists can use PPT-DB to accurately predict (via sequence homology):
1) Secondary structure (helices, beta strands, beta turns, transmembrane helices, etc.)
2) 3D structure parameters (disulfide bonding pairs, contact order, salt bridges)
3) Protein dynamics (order parameters, RMSF, B-factors)
4) Protein signaling motifs (gram +/gram - and eukaryotic signal peptides)
5) Protein folding rates (ln(k), contact order, secondary structure content)

Software Developers can use PPT-DB as a one-stop-shop to obtain high quality data sets to train, test, evaluate and validate protein property prediction software including:
1) Secondary structure prediction software
2) Protein flexibility/epitope prediction software
3) Transmembrane helix, signal peptide and beta barrel prediction software
4) 3D structure prediction software
5) Miscellaneous properties (protein folding rates, disulfide bond pairs, contact order)
Reference:
PPT-DB: the protein property prediction and testing database. Nucleic Acids Research 2008 36(Database issue):D222-D229.

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