NMR paper NMR refinement and peptide folding using the GROMACS software

		BioNMR > Educational resources > Journal club
[NMR paper] NMR refinement and peptide folding using the GROMACS software

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

03-29-2021, 08:10 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,734

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 refinement and peptide folding using the GROMACS software

NMR refinement and peptide folding using the GROMACS software

Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins and nucleic acids. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model distance...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
NMR refinement and peptide folding using the GROMACS software NMR refinement and peptide folding using the GROMACS software Abstract Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins and nucleic acids. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model...	nmrlearner	Journal club	0	03-28-2021 04:24 PM
[NMR paper] SPR and NMR characterization of the molecular interaction between A9 peptide and a model system of HER2 receptor: A fragment approach for selecting peptide structures specific for their target. SPR and NMR characterization of the molecular interaction between A9 peptide and a model system of HER2 receptor: A fragment approach for selecting peptide structures specific for their target. Related Articles SPR and NMR characterization of the molecular interaction between A9 peptide and a model system of HER2 receptor: A fragment approach for selecting peptide structures specific for their target. J Pept Sci. 2020 Feb;26(2):e3231 Authors: De Luca S, Verdoliva V, Saviano M, Fattorusso R, Diana D Abstract The binding process of...	nmrlearner	Journal club	0	08-20-2020 02:48 PM
Exploring Folding Cooperativity of a Repeat Protein Folding by 2D-NMR Detected Pressure Perturbation Exploring Folding Cooperativity of a Repeat Protein Folding by 2D-NMR Detected Pressure Perturbation Publication date: 16 February 2016 Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1</br> Author(s): Martin J. Fossat, Angel Garcia, Doug Barrick, Christian Roumestand, Catherine A. Royer</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	02-17-2016 07:50 PM
[NMR tweet] NMR Data-Acquisition Software: Agilent introduced the latest version of its data-acquisition software for nuclear magnetic resonance ... NMR Data-Acquisition Software: Agilent introduced the latest version of its data-acquisition software for nuclear magnetic resonance ... Published by davidp98 (David P.) on 2013-04-16T05:52:41Z Source: Twitter	nmrlearner	Twitter NMR	0	04-16-2013 06:22 AM
Biomolecular structure refinement using the GROMOS simulation software Biomolecular structure refinement using the GROMOS simulation software Abstract For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, 3 J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions...	nmrlearner	Journal club	1	08-25-2011 07:03 AM
Transferred NOESY NMR studies of biotin mimetic peptide (FSHPQNT) bound to streptavidin: A structural model for studies of peptide-protein interactions. Transferred NOESY NMR studies of biotin mimetic peptide (FSHPQNT) bound to streptavidin: A structural model for studies of peptide-protein interactions. Transferred NOESY NMR studies of biotin mimetic peptide (FSHPQNT) bound to streptavidin: A structural model for studies of peptide-protein interactions. Chem Biol Drug Des. 2011 Feb 5; Authors: Gizachew D, Dratz E Protein-protein interactions control signaling, specific adhesion and many other biological functions. The three dimensional structures of the interfaces and bound ligand can be...	nmrlearner	Journal club	0	02-08-2011 06:28 PM
[NMR paper] The cisproline(i - 1)-aromatic(i) interaction: folding of the Ala-cisPro-Tyr peptide The cisproline(i - 1)-aromatic(i) interaction: folding of the Ala-cisPro-Tyr peptide characterized by NMR and theoretical approaches. Related Articles The cisproline(i - 1)-aromatic(i) interaction: folding of the Ala-cisPro-Tyr peptide characterized by NMR and theoretical approaches. J Biomol NMR. 2000 May;17(1):63-77 Authors: Nardi F, Kemmink J, Sattler M, Wade RC Cisproline(i - 1)-aromatic(i) interactions have been detected in several short peptides in aqueous solution by analysis of anomalous chemical shifts measured by 1H-NMR spectroscopy....	nmrlearner	Journal club	0	11-18-2010 09:15 PM
Installation of GROMACS 3.3.1 on Dell Inspiron 6400 with Fedora Core 6, Test 3, Dual Core processor This is not really a "hard-core NMR topic" but it could be useful for people who try to complement dynamics data from NMR relaxation experiments with MD simulations. I had really hard time trying to install the newer versions of Gromacs 3.3 and 3.3.1 on my laptop (Dell Inspiron 6400 Dual Core processor) . The laptop used to run Suse 10.1 that was recently replaced with Fedora Core 6 Test 3 (that finally supports Intel integrated mobile 945 video cards). With both OS, Gromacs 3.3.x could be installed, however, its sub-program "genion" failed (the program never ends while consuming 100%...	administrator	Molecular Dynamics programs	0	10-04-2006 11:50 AM

« 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