Finding protein function from its NMR structure

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Finding protein function from its NMR structure

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

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09-14-2005, 07:35 PM

nmrlearner

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Finding protein function from its NMR

For proteomics folks who gamble with their careers by promising discovery of protein function from NMR structures that may not look like any known proteins.

Find the best structural matches in a protein database
DALI
CE
DEJAVU

Align structure of your protein with several proteins of your interest
MASS
MaltiProt
CEMC
CATH

Pairwise comparison of protein structures
SuperPose
FAST
K2SA
CE
Protein3DFit
SSAP

relevant links:
http://www.csb.yale.edu/poststructure/

09-19-2006, 12:11 PM

mrevingt

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Try ProFunc from Janet Thornton's group

"It uses both sequence- and structure-based methods to try to provide clues as the the protein's likely or possible function. Often, where one method fails to provide any functional insight another may be more helpful."

http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/

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