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Ab initio:
GeNMR
Cyana
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Fragment-based:
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Template-based:
GeNMR
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Refinement:
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Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
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Promega- Proline
Secondary structure from chemical shifts:
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Flexibility from chemical shifts:
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Interactions from chemical shifts:
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Chemical shifts re-referencing:
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SAVES2 or SAVES4
Vadar
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V-NMR
Flexibility from structure:
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Methyl S2
B-factor
Molecular dynamics:
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Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
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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:
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Solid-state NMR:
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Default Enhanced protein fold recognition using secondary structure information from NMR.

Enhanced protein fold recognition using secondary structure information from NMR.

Related Articles Enhanced protein fold recognition using secondary structure information from NMR.

Protein Sci. 1999 May;8(5):1127-33

Authors: Ayers DJ, Gooley PR, Widmer-Cooper A, Torda AE

NMR offers the possibility of accurate secondary structure for proteins that would be too large for structure determination. In the absence of an X-ray crystal structure, this information should be useful as an adjunct to protein fold recognition methods based on low resolution force fields. The value of this information has been tested by adding varying amounts of artificial secondary structure data and threading a sequence through a library of candidate folds. Using a literature test set, the threading method alone has only a one-third chance of producing a correct answer among the top ten guesses. With realistic secondary structure information, one can expect a 60-80% chance of finding a homologous structure. The method has then been applied to examples with published estimates of secondary structure. This implementation is completely independent of sequence homology, and sequences are optimally aligned to candidate structures with gaps and insertions allowed. Unlike work using predicted secondary structure, we test the effect of differing amounts of relatively reliable data.

PMID: 10338023 [PubMed - indexed for MEDLINE]



Source: PubMed
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