automated backbone assignment

		BioNMR > Educational resources > NMR Questions and Answers
automated backbone assignment

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

08-07-2006, 01:07 AM

sarun

Junior Member

Join Date: Aug 2006

Posts: 2

Points: 24, Level: 1

Level up: 47%, 26 Points needed

Activity: 0%

NMR Credits: 0

NMR Points: 24

Downloads: 0

Uploads: 0

Answered:

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

Thanks.

Did you find this post helpful?

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]

08-08-2006, 04:49 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,776

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

Provided Answers: 3

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

Quote:

Did you find this post helpful?

03-30-2007, 03:21 PM

premprakash premprakash is offline

Junior Member

Join Date: Mar 2007

Posts: 7

Points: 24, Level: 1

Level up: 47%, 26 Points needed

Activity: 0%

NMR Credits: 0

NMR Points: 24

Downloads: 0

Uploads: 0

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

Did you find this post helpful?

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

« 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