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

		BioNMR > NMR community > News from NMR blogs
[KPWU blog] statistics of NMR/X-ray determined protein structures in PDB (up to May 10, 2011)

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

05-17-2011, 08:30 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

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.

Did you find this post helpful?

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

« 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 Off Trackbacks are Off Pingbacks are Off Refbacks are Off