BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 08-22-2011, 05:22 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default 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 and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.
  • Content Type Journal Article
  • Category Article
  • Pages 1-17
  • DOI 10.1007/s10858-011-9534-0
  • Authors
    • Nathan Schmid, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
    • Jane R. Allison, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
    • Jožica Dolenc, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
    • Andreas P. Eichenberger, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
    • Anna-Pitschna E. Kunz, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland
    • Wilfred F. van Gunsteren, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland

Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

  #2  
Unread 08-25-2011, 07:03 AM
Junior Member
 
Join Date: Aug 2011
Posts: 3
Points: 16, Level: 1
Points: 16, Level: 1 Points: 16, Level: 1 Points: 16, Level: 1
Level up: 31%, 34 Points needed
Level up: 31% Level up: 31% Level up: 31%
Activity: 15.8%
Activity: 15.8% Activity: 15.8% Activity: 15.8%
NMR Credits: 0
NMR Points: 16
Downloads: 0
Uploads: 0
Default

This article is exactly what I needed


Reply With Quote


Did you find this post helpful? Yes | No
Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[CNS Yahoo group] water refinement problem - broken structure
water refinement problem - broken structure Dear all, I'm trying to perform water refinement for the very first time (new CNS user), on an NMR ensemble of CYANA calculated protein structures but the end More...
nmrlearner News from other NMR forums 0 07-18-2011 09:41 AM
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation. Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation. Biophys J. 2010 Nov 17;99(10):3282-9 Authors: Toraya S, Javkhlantugs N, Mishima D, Nishimura K, Ueda K, Naito A Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to...
nmrlearner Journal club 0 03-03-2011 12:34 PM
The structure of the talin/integrin complex at a lipid bilayer: an NMR and MD simulation study.
The structure of the talin/integrin complex at a lipid bilayer: an NMR and MD simulation study. The structure of the talin/integrin complex at a lipid bilayer: an NMR and MD simulation study. Structure. 2010 Oct 13;18(10):1280-8 Authors: Kalli AC, Wegener KL, Goult BT, Anthis NJ, Campbell ID, Sansom MS Integrins are cell surface receptors crucial for cell migration and adhesion. They are activated by interactions of the talin head domain with the membrane surface and the integrin ? cytoplasmic tail. Here, we use coarse-grained molecular dynamic...
nmrlearner Journal club 0 03-03-2011 12:34 PM
[NMR paper] Essential spaces defined by NMR structure ensembles and molecular dynamics simulation
Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap. Related Articles Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap. Proteins. 1998 Jun 1;31(4):370-82 Authors: Abseher R, Horstink L, Hilbers CW, Nilges M Large concerted motions of proteins which span its "essential space," are an important component of protein dynamics. We investigate to what extent structure ensembles generated with standard structure calculation...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[CNS Yahoo group] refinement of large low resolution structure
refinement of large low resolution structure Hi all, I have a structure at 2.65A that I'm in the process of refining. It's a complex that has ~1100 residues total, and what looks like a fair amount of More...
nmrlearner News from other NMR forums 0 10-22-2010 07:36 PM
[NMR paper] NMR chemical shifts and structure refinement in proteins.
NMR chemical shifts and structure refinement in proteins. Related Articles NMR chemical shifts and structure refinement in proteins. J Biomol NMR. 1993 Sep;3(5):607-12 Authors: Laws DD, de Dios AC, Oldfield E Computation of the 13C alpha chemical shifts (or shieldings) of glycine, alanine and valine residues in bovine and Drosophila calmodulins and Staphylococcal nuclease, and comparison with experimental values, is reported using a gauge-including atomic orbital quantum-chemical approach. The full approximately 24 ppm shielding range is...
nmrlearner Journal club 0 08-22-2010 03:01 AM
structure refinement after cyana
Can anybody tell me, how to energy minimize a CYANA calculated average structure. I used model_minimize.inp from CNS, but is there any other method generally used by the CYANA users. Also, how can I get the bonds, impropers and angle violation (rmsds) information on the CYANA calculated structures. Does CYANA has any program to do it. Please help me with it. Thank you.
sarun NMR Questions and Answers 0 11-20-2008 03:41 AM
Structure refinement based on adaptive restraints using local-elevation simulation
Biomolecular structure refinement based on adaptive restraints using local-elevation simulation Markus Christen, Bettina Keller and Wilfred F. van Gunsteren Journal of Biomolecular NMR; 2007; 39(4) pp 265 - 273 Abstract: Introducing experimental values as restraints into molecular dynamics (MD) simulation to bias the values of particular molecular properties, such as nuclear Overhauser effect intensities or distances, dipolar couplings, 3 J-coupling constants, chemical shifts or crystallographic structure factors, towards experimental values is a widely used structure refinement...
linawaed Journal club 0 08-04-2008 04:29 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 04:02 PM.


Map