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

Go Back   BioNMR > Educational resources > NMR Questions and Answers
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 08-07-2006, 01:07 AM
Junior Member
 
Join Date: Aug 2006
Posts: 2
Points: 24, Level: 1
Points: 24, Level: 1 Points: 24, Level: 1 Points: 24, Level: 1
Level up: 47%, 26 Points needed
Level up: 47% Level up: 47% Level up: 47%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 24
Downloads: 0
Uploads: 0
Default Answered:

Can anyone suggest me a most commonly used and worthful software for automated backbone assignment of triple labeled proteins.

Thanks.
Reply With Quote


Did you find this post helpful? Yes | No
Best Answer - Posted by nmrlearner
I have not tried it myself but many people, whom I had a chance to ask this question, recommended MARS.


Quote:
Originally posted by sarun@Aug 6 2006, 06:07 PM
Can anyone suggest me a most commonly used and worthful software for automated backbone assignment of triple labeled proteins.

Thanks.
[snapback]179[/snapback]

  #2  
Unread 08-08-2006, 04:49 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,063
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
Provided Answers: 3
Default

I have not tried it myself but many people, whom I had a chance to ask this question, recommended MARS.


Quote:
Originally posted by sarun@Aug 6 2006, 06:07 PM
Can anyone suggest me a most commonly used and worthful software for automated backbone assignment of triple labeled proteins.

Thanks.
[snapback]179[/snapback]
Reply With Quote


Did you find this post helpful? Yes | No
  #3  
Unread 03-30-2007, 03:21 PM
premprakash's Avatar
Junior Member
 
Join Date: Mar 2007
Posts: 7
Points: 24, Level: 1
Points: 24, Level: 1 Points: 24, Level: 1 Points: 24, Level: 1
Level up: 47%, 26 Points needed
Level up: 47% Level up: 47% Level up: 47%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 24
Downloads: 0
Uploads: 0
Default Rdc

Hi!
I wanted to know about using PALES for measuring the dipolar couplings
I have the program on a Linux SuSe , I do not have C' Compiler or fortran. are they require to get the PALES working.
When i try, it just stops before giving the dipoar coupling , and reports zero DC.

Cheers!
Prem Prakash Pathak
Reply With Quote


Did you find this post helpful? Yes | No
Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Error tolerant NMR backbone resonance assignment and automated structure generation.
Error tolerant NMR backbone resonance assignment and automated structure generation. Error tolerant NMR backbone resonance assignment and automated structure generation. J Bioinform Comput Biol. 2011 Feb;9(1):15-41 Authors: Alipanahi B, Gao X, Karakoc E, Li SC, Balbach F, Feng G, Donaldson L, Li M Error tolerant backbone resonance assignment is the cornerstone of the NMR structure determination process. Although a variety of assignment approaches have been developed, none works sufficiently well on noisy fully automatically picked peaks to enable...
nmrlearner Journal club 0 02-18-2011 08:07 PM
[NMR paper] Protein NMR structure determination with automated NOE assignment using the new softw
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. Related Articles Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol. 2002 May 24;319(1):209-27 Authors: Herrmann T, Güntert P, Wüthrich K Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Automated NMR determination of protein backbone dihedral angles from cross-correlated
Automated NMR determination of protein backbone dihedral angles from cross-correlated spin relaxation. Related Articles Automated NMR determination of protein backbone dihedral angles from cross-correlated spin relaxation. J Biomol NMR. 2002 Apr;22(4):349-63 Authors: Kloiber K, Schüler W, Konrat R The simultaneous interpretation of a suite of dipole-dipole and dipole-CSA cross-correlation rates involving the backbone nuclei 13Calpha, 1Halpha, 13CO, 15N and 1HN can be used to resolve the ambiguities associated with each individual...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Tools for the automated assignment of high-resolution three-dimensional protein NMR s
Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques. Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques. J Biomol NMR. 1997 Oct;10(3):207-19 Authors: Croft D, Kemmink J, Neidig KP, Oschkinat H One of the major bottlenecks in the determination of proteinstructures by NMR is in the evaluation of the data produced by theexperiments. An important step in this process is assignment, where...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain
Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment. Related Articles Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment. J Chem Inf Comput Sci. 1997 May-Jun;37(3):467-77 Authors: Li KB, Sanctuary BC A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.
Application of neural networks to automated assignment of NMR spectra of proteins. Related Articles Application of neural networks to automated assignment of NMR spectra of proteins. J Biomol NMR. 1994 Jan;4(1):35-46 Authors: Hare BJ, Prestegard JH Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.
Application of neural networks to automated assignment of NMR spectra of proteins. Related Articles Application of neural networks to automated assignment of NMR spectra of proteins. J Biomol NMR. 1994 Jan;4(1):35-46 Authors: Hare BJ, Prestegard JH Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...
nmrlearner Journal club 0 08-22-2010 03:33 AM
MONTE: a program for automated NMR assignment
MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. Hitchens TK, Lukin JA, Zhan Y, McCallum SA, Rule GS. Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA. J Biomol NMR. 2003 Jan;25(1):1-9. http://www.bionmr.com/forum/style_images/monte.gif Monte website
nmrlearner NMR software 0 07-17-2005 03:04 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 - 2017, 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 10:12 PM.


Map