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 NMR blogs
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 05-17-2011, 08:30 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 statistics of NMR/X-ray determined protein structures in PDB (up to May 10, 2011)

statistics of NMR/X-ray determined protein structures in PDB (up to May 10, 2011)

Two brief plots of protein structures (protein-DNA/RNA/ligand complexes are excluded) determined by either X-ray or NMR. Structures determined by hybrid method are not counted in the two plots. The dataset was obtain from PDB based on its released statistics by May 10th, 2011. Molecules with sequence length longer than 1200 residues are also excluded. There [...]

Go to KPWU blog to read complete post.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[Question from NMRWiki Q&A forum] What is the violation statistics best practice?
What is the violation statistics best practice? I am wondering whether anyone knows if there is an established "best practice" on how many restraint violations (distance and dihedral angle) are acceptable in a refined ensemble. Specifically, I currently have an ensemble average of 4.8 distance restraint violations greater than 0.2 Angstroms, with no violations greater than 0.4 Angstroms. For dihedral angles, I have an ensemble average of 1.5 violations greater than 5 degrees, with the greatest violation having a value of 7.9 degrees. Do these values seem reasonable? Check if...
nmrlearner News from other NMR forums 0 07-19-2011 09:52 AM
[NMR tweet] Baker Lab. Large protein structures can now b determined by incorporating backbone-only NMR (Nuclear Magnetic Resonance) data into Rosetta..
Baker Lab. Large protein structures can now b determined by incorporating backbone-only NMR (Nuclear Magnetic Resonance) data into Rosetta.. Published by zukaraSophia (A, just A) on 2011-06-14T19:46:43Z Source: Twitter
nmrlearner Twitter NMR 0 06-14-2011 07:50 PM
[NMR paper] Relative stability of protein structures determined by X-ray crystallography or NMR s
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study. Related Articles Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study. Proteins. 2003 Oct 1;53(1):111-20 Authors: Fan H, Mark AE The relative stability of protein structures determined by either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy has been investigated by using molecular dynamics simulation...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Evaluation of the utility of NMR structures determined from minimal NOE-based restrai
Evaluation of the utility of NMR structures determined from minimal NOE-based restraints for structure-based drug design, using MMP-1 as an example. Related Articles Evaluation of the utility of NMR structures determined from minimal NOE-based restraints for structure-based drug design, using MMP-1 as an example. Biochemistry. 2000 Nov 7;39(44):13365-75 Authors: Huang X, Moy F, Powers R The application of deuterium labeling and residual dipolar coupling constants in combination with other structural information has demonstrated the potential...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] An assessment of the precision and accuracy of protein structures determined by NMR.
An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors. J Mol Biol. 1994 Jun 24;239(5):601-7 Authors: Zhao D, Jardetzky O We tested the dependence of the accuracy and precision of calculated NMR structures on the errors of the distance constraints...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] An assessment of the precision and accuracy of protein structures determined by NMR.
An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors. J Mol Biol. 1994 Jun 24;239(5):601-7 Authors: Zhao D, Jardetzky O We tested the dependence of the accuracy and precision of calculated NMR structures on the errors of the distance constraints...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Comparison of protein structures determined by NMR in solution and by X-ray diffracti
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals. Related Articles Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals. Q Rev Biophys. 1992 Aug;25(3):325-77 Authors: Billeter M
nmrlearner Journal club 0 08-21-2010 11:45 PM
Major groove width variations in RNA structures determined by NMR and impact of 13C r
Abstract Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by 1Hâ?? 1H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of...
nmrlearner Journal club 0 08-14-2010 04:19 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 Off
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 07:33 AM.


Map