NMR paper Peakr: Simulating solid-state NMR spectra of proteins.

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[NMR paper] Peakr: Simulating solid-state NMR spectra of proteins.

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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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03-16-2013, 03:18 PM

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Peakr: Simulating solid-state NMR spectra of proteins.

Peakr: Simulating solid-state NMR spectra of proteins.

Related Articles Peakr: Simulating solid-state NMR spectra of proteins.

Bioinformatics. 2013 Mar 14;

Authors: Schneider R, Odronitz F, Hammesfahr B, Hellkamp M, Kollmar M

Abstract
MOTIVATION: When analyzing solid-state NMR spectra of proteins, assignment of resonances to nuclei and derivation of restraints for 3D structure calculations are challenging and time-consuming processes. Simulated spectra that have been calculated based on, e.g., chemical shift predictions and structural models can be of considerable help. Existing solutions are typically limited in the type of experiment they can consider and difficult to adapt to different settings. RESULTS: Here, we present Peakr, a software to simulate solid-state NMR spectra of proteins. It can generate simulated spectra based on numerous common types of internuclear correlations relevant for assignment and structure elucidation, can compare simulated and experimental spectra, and produces lists and visualizations useful for analyzing measured spectra. Compared to other solutions it is fast, versatile and user friendly.Availability and Implementation: Peakr is maintained under the GPL license and can be accessed at http://www.peakr.org. The source code can be obtained upon request from the authors. CONTACT: robert.schneider@ibs.fr, mako@nmr.mpibpc.mpg.de.

PMID: 23493322 [PubMed - as supplied by publisher]

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