Script to obtain order parameters from a structure

		BioNMR > Software > Molecular modeling software > NMR dynamics
Script to obtain order parameters from a structure

Webservers

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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

05-07-2005, 09:21 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,731

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

A Python script for prediction of order paramter from a structure is available from this website.

The script is based on the following paper

F. Zhang and R. Brüschweiler (2002) "Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins" J. Am. Chem. Soc. 124(43), 12654-12655.

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion. NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion. NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion. J Biomol NMR. 2011 May;50(1):59-70 Authors: Johnson E Abstract NMR order parameters are calculated from molecular dynamics computer simulations of ubiquitin and the apo (Ca(2+)-free) state of calbindin D(9k). Calculations are performed in an expanding reference frame so as to discriminate between the effects of...	nmrlearner	Journal club	0	08-20-2011 03:31 PM
NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion Abstract NMR order parameters are calculated from molecular dynamics computer simulations of ubiquitin and the apo (Ca2+-free) state of calbindin D9k. Calculations are performed in an expanding reference frame so as to discriminate between the effects of short- and long-range motions. This approach reveals that the dominant contributions to the order parameters are short-range. Longer-range contributions are limited to specific sites, many of which have been recognized in...	nmrlearner	Journal club	0	04-24-2011 03:40 AM
[NMR paper] Determination of protein structures consistent with NMR order parameters. Determination of protein structures consistent with NMR order parameters. Related Articles Determination of protein structures consistent with NMR order parameters. J Am Chem Soc. 2004 Jul 7;126(26):8090-1 Authors: Best RB, Vendruscolo M Order parameters obtained from NMR experiments characterize distributions of bond vector orientations. Their interpretation, however, usually requires the assumption of a particular motional model. We propose a multiple-copy simulation method in which the experimental order parameters are used as restraints in...	nmrlearner	Journal club	0	11-24-2010 09:51 PM
[NMR paper] Temperature dependence of NMR order parameters and protein dynamics. Temperature dependence of NMR order parameters and protein dynamics. Related Articles Temperature dependence of NMR order parameters and protein dynamics. J Am Chem Soc. 2003 Sep 17;125(37):11158-9 Authors: Massi F, Palmer AG The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
[NMR paper] Correlation between 2H NMR side-chain order parameters and sequence conservation in g Correlation between 2H NMR side-chain order parameters and sequence conservation in globular proteins. Related Articles Correlation between 2H NMR side-chain order parameters and sequence conservation in globular proteins. J Am Chem Soc. 2003 Jul 30;125(30):9004-5 Authors: Mittermaier A, Davidson AR, Kay LE Side-chain 2H NMR relaxation data have been collected for the SH3 domain from the Fyn tyrosine kinase and analyzed with respect to sequence preference and per-residue solvent accessibility. Residues that are highly preferred at a given...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
[NMR paper] Protein dynamics using frequency-dependent order parameters from analysis of NMR rela Protein dynamics using frequency-dependent order parameters from analysis of NMR relaxation data. Related Articles Protein dynamics using frequency-dependent order parameters from analysis of NMR relaxation data. J Magn Reson. 2003 Mar;161(1):118-25 Authors: Idiyatullin D, Daragan VA, Mayo KH A novel approach is described to analyze NMR relaxation data on proteins. This method introduces the frequency-dependent order parameter, S(2)(omega), in order to estimate contributions to the generalized order parameter S(2) from different motional...	nmrlearner	Journal club	0	11-24-2010 09:01 PM
[NMR paper] Contact model for the prediction of NMR N-H order parameters in globular proteins. Contact model for the prediction of NMR N-H order parameters in globular proteins. Related Articles Contact model for the prediction of NMR N-H order parameters in globular proteins. J Am Chem Soc. 2002 Oct 30;124(43):12654-5 Authors: Zhang F, Brüschweiler R An analytical relationship is presented for the estimation of NMR S2 order parameters of N-HN vectors of the protein backbone from high-resolution protein structures. The relationship solely depends on close contacts of the peptide plane to the rest of the protein. Application of the...	nmrlearner	Journal club	0	11-24-2010 08:58 PM
[NMR paper] Simple multidimensional NMR experiments to obtain different types of one-bond dipolar Simple multidimensional NMR experiments to obtain different types of one-bond dipolar couplings simultaneously. Related Articles Simple multidimensional NMR experiments to obtain different types of one-bond dipolar couplings simultaneously. J Biomol NMR. 2001 Jan;19(1):63-7 Authors: de Alba E, Suzuki M, Tjandra N In order to measure residual dipolar couplings, the molecule under study has to be partially oriented in the presence of the magnetic field. It has been observed that some protein samples are not stable under the conditions imposed by...	nmrlearner	Journal club	0	11-19-2010 08:32 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off