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

Go Back   BioNMR > NMR community > News from other NMR forums
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 02-08-2015, 01:21 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 building chains of resonance groups from connectivities

building chains of resonance groups from connectivities

Greetings,

Given a dictionary of connectivities of the following form:

residue i -> possible residues i-1 :

54 -> 23, 45, 6712 -> 78, 543 -> 4 ,7etc.

where the number above are not residue number, but resonance groups. I want to find all possible chains of resonance groups, for example:

(38, 50, 76, 63, 78)(38, 50, 76, 63, 45, 90)(38, 12, 30)(64, 53, 60)(64, 53, 20, 44)etc.

I think this is a common problem in NMR, so I would like to ask if anyone knows any program or Sparky plugin that does a similar job to use it as a reference.



Check if somebody has answered this question on NMRWiki QA forum
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection
Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection Abstract Protein dynamics on the microsecondâ??millisecond time scales often play a critical role in biological function. NMR relaxation dispersion experiments are powerful approaches for investigating biologically relevant dynamics with site-specific resolution, as shown by a growing number of publications on enzyme catalysis, protein folding, ligand binding, and allostery. To date, the majority of studies has probed the...
nmrlearner Journal club 0 06-19-2014 10:21 PM
[NMR images] product diabetes device country china time 2006 add 610 building 2 no ...
http://www.china-vango.com/UPLOAD/201092864358689.jpg 15/03/2014 12:34:51 PM GMT product diabetes device country china time 2006 add 610 building 2 no ... More...
nmrlearner NMR pictures 0 03-15-2014 12:34 PM
A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins
A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins Abstract A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-glucose and subsaturating amounts of 2-methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional 1H-13C correlation spectra. Protein samples are conveniently prepared using the same media composition as the...
nmrlearner Journal club 0 02-06-2011 07:42 PM
[NMR tweet] in late 1945 in "Building 20", NMR (nuclear magnetic resonance) spectroscopy was disc
in late 1945 in "Building 20", NMR (nuclear magnetic resonance) spectroscopy was discovered @ MIT by Harvard... http://fb.me/OJmpsZaB Published by Lizzard0126 (Liz O'Day) on 2010-11-24T02:55:51Z Source: Twitter
nmrlearner Twitter NMR 0 11-24-2010 03:00 AM
[NMR paper] Toward direct determination of conformations of protein building units from multidime
Toward direct determination of conformations of protein building units from multidimensional NMR experiments part II: a theoretical case study of formyl-L-valine amide. Related Articles Toward direct determination of conformations of protein building units from multidimensional NMR experiments part II: a theoretical case study of formyl-L-valine amide. Chemistry. 2001 Mar 2;7(5):1069-83 Authors: Perczel A, Császár AG Chemical shielding anisotropy tensors have been determined for all twenty-seven characteristic conformers of For-L-Val-NH2 using...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[Question from NMRWiki Q&A forum] HCCH-Tocsy connectivities
HCCH-Tocsy connectivities What I see from this picture (linked from www.protein-nmr.org.uk): http://www.protein-nmr.org.uk/pictures/experiment_types/hcch_tocsy.png that shows an HCCH-TOCSY magnetisation transfer I do not see any transfer from HD to HB, but in my peaks I see a peak that seems it can be connected az Leu CB-HB2-HD22Can I have these peaks in HCCH-TOCSY? would you please introduce me a reference that tell me what kind of connection can be visible in HC(C)H-Tocsy
nmrlearner News from other NMR forums 0 11-17-2010 06:08 PM
[NMR tweet] New Chemistry Building Comes to Life As Researchers Begin Move Into Space: A nuclear
New Chemistry Building Comes to Life As Researchers Begin Move Into Space: A nuclear magnetic resonance imaging (N... http://bit.ly/dzViuK Published by Sun_raven (sun raven) on 2010-09-15T17:59:27Z Source: Twitter
nmrlearner Twitter NMR 0 09-15-2010 06:40 PM
[NMR paper] Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains
Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains of an intact glycoprotein. Application of gradient-enhanced natural abundance 1H-13C HSQC and HSQC-TOCSY to the alpha-subunit of human chorionic gonadotropin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains of an intact glycoprotein. Application of gradient-enhanced natural abundance 1H-13C HSQC and HSQC-TOCSY to the alpha-subunit of...
nmrlearner Journal club 0 08-22-2010 03:29 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 01:38 PM.


Map