NMR Restrained Protein Structure Calculations in Implicit Water/Membrane*Environments

		BioNMR > Educational resources > Journal club
*NMR Restrained Protein Structure Calculations in Implicit Water/MembraneEnvironments**

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

02-17-2016, 07:50 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,184

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

NMR Restrained Protein Structure Calculations in Implicit Water/Membrane*Environments

NMR Restrained Protein Structure Calculations in Implicit Water/Membrane*Environments

Publication date: 16 February 2016
Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1

Author(s): Ye Tian, Charles Schwieters, Stanley Opella, Francesca Marassi

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins. A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins. A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins. Biophys J. 2015 Aug 4;109(3):574-585 Authors: Tian Y, Schwieters CD, Opella SJ, Marassi FM Abstract The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the...	nmrlearner	Journal club	0	08-06-2015 10:24 AM
A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins Publication date: 4 August 2015 Source:Biophysical Journal, Volume 109, Issue 3</br> Author(s): Ye Tian, CharlesD. Schwieters, StanleyJ. Opella, Francesca*M. Marassi</br> The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because...	nmrlearner	Journal club	0	08-05-2015 08:21 PM
[NMR paper] Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation. J Biomol NMR. 2015 Jul 5; Authors: Marassi FM, Ding Y, Schwieters CD, Tian Y, Yao Y Abstract The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement...	nmrlearner	Journal club	0	07-06-2015 04:35 PM
Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation Abstract The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot,...	nmrlearner	Journal club	0	07-05-2015 02:07 AM
NMR-Restrained Structure Calculations of Membrane Proteins in Implicit Lipid Bilayer Membranes NMR-Restrained Structure Calculations of Membrane Proteins in Implicit Lipid Bilayer Membranes Publication date: 27 January 2015 Source:Biophysical Journal, Volume 108, Issue 2, Supplement 1</br> Author(s): Ye Tian , Charles Schwieters , Stanley Opella , Francesca Marassi</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	01-28-2015 05:28 PM
NMR-Restrained Protein Structure Calculations in Implicit Environment NMR-Restrained Protein Structure Calculations in Implicit Environment Publication date: 28 January 2014 Source:Biophysical Journal, Volume 106, Issue 2, Supplement 1</br> Author(s): Ye Tian , Charles Schwieters , Stanley J. Opella , Francesca M. Marassi</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	01-29-2014 12:50 AM
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside...	nmrlearner	Journal club	0	09-26-2011 06:42 AM
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. J Biomol NMR. 2011 Sep 22; Authors: Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular...	nmrlearner	Journal club	0	09-23-2011 05:30 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