NMR paper The accuracy of NMR protein structures in the Protein Data Bank

		BioNMR > Educational resources > Journal club
[NMR paper] The accuracy of NMR protein structures in the Protein Data Bank

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

08-01-2021, 04:02 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,188

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

The accuracy of NMR protein structures in the Protein Data Bank

The accuracy of NMR protein structures in the Protein Data Bank

The program ANSURR measures the accuracy of NMR structures by comparing rigidity obtained from experimental backbone chemical shifts and from structures. We report on ANSURR analysis of 7,000 PDB NMR ensembles within the Protein Data Bank, which can be found at ansurr.com. The accuracy of NMR structures progressively improved up until 2005, but since then, it has plateaued. Most structures have accurate secondary structure, but are generally too floppy, particularly in loops. Thus, there is a...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures. Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures. Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures. J Am Chem Soc. 2014 Jan 6; Authors: Mao B, Tejero R, Baker D, Montelione GT Abstract We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement...	nmrlearner	Journal club	0	01-08-2014 11:23 AM
[CNS Yahoo group] A little bit of sunshine from the Protein Data Bank in Europe (pdbe. A little bit of sunshine from the Protein Data Bank in Europe (pdbe. Hi all, Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org) releases new, improved and updated versions of its tools and resources. Below is More...	nmrlearner	News from other NMR forums	0	07-13-2012 09:15 AM
PDBe Protein Data Bank in Europe PDBe Protein Data Bank in Europe PDBe, Protein Data Bank in Europe, is part of the EBI-EMBL, and serves as a European resource for PDB protein structure deposition annotation to the wwPDB. We provide powerful 3D structure search services and analysis tools for PDB data related to structures of proteins, nucleic acids, carbohydrates, small molecules, ligands, drugs and antibiotics.We integrate data from Interpro, Uniprot, GO, CATH, SCOP, Pfam, etc. through the SIFTS project to enrich the data held in the Protein Data Bank More...	nmrlearner	General	0	12-14-2011 07:14 PM
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Open Biochem J. 2010;4:83-95 Authors: Sikic K, Tomic S, Carugo O Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in...	nmrlearner	Journal club	0	02-05-2011 05:28 PM
[NMR paper] Assessing precision and accuracy of protein structures derived from NMR data. Assessing precision and accuracy of protein structures derived from NMR data. Related Articles Assessing precision and accuracy of protein structures derived from NMR data. Proteins. 2005 Jun 1;59(4):655-61 Authors: Snyder DA, Bhattacharya A, Huang YJ, Montelione GT	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[CNS Yahoo group] Job opportunities at the Protein Data Bank in Europe (pdbe.org) Job opportunities at the Protein Data Bank in Europe (pdbe.org) Hi all, We have two new openings at the Protein Data Bank in Europe (http://pdbe.org - part of the European Bioinformatics Institute in Cambridge, UK) to work More...	nmrlearner	News from other NMR forums	0	11-12-2010 04:34 AM
[CNS Yahoo group] Job opportunities at the Protein Data Bank in Europe Job opportunities at the Protein Data Bank in Europe There are three more vacancies coming up at the Protein Data Bank in Europe (PDBe; pdbe.org): - Head of PDBe Deposition and Annotation More...	nmrlearner	News from other NMR forums	0	08-21-2010 03:26 PM
[CNS Yahoo group] Protein Data Bank in Europe roadshows and tutorials Protein Data Bank in Europe roadshows and tutorials The Protein Data Bank in Europe (PDBe; http://pdbe.org/) offers a number of educational resources as part of its wider mandate for outreach and training within More...	nmrlearner	News from other NMR forums	0	08-21-2010 03:26 PM

« 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