Automatic Protein Structure Determination from Sparse NMR Spectroscopy Data

		BioNMR > Educational resources > Journal club
Automatic Protein Structure Determination from Sparse NMR Spectroscopy Data

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

02-17-2016, 07:50 PM

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

Automatic Protein Structure Determination from Sparse NMR Spectroscopy Data

Automatic Protein Structure Determination from Sparse NMR Spectroscopy Data

Publication date: 16 February 2016
Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1

Author(s): Justin L. MacCallum, Yuefeng Tang, Y. Janet Huang, Gaetano T. Montelione

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Protein structure determination by combining sparse NMR data with evolutionary ... - Nature.com Protein structure determination by combining sparse NMR data with evolutionary ... - Nature.com http://www.bionmr.com//t0.gstatic.com/images?q=tbn:ANd9GcQt4ROxcirbsmGx2eocNyxOy2KXS28zU0-Tl-RnYcmF9nTAEFxp8hFacTn-QpyLN8UilrT40VY Nature.com <img alt="" height="1" width="1"> Protein structure determination by combining sparse NMR data with evolutionary ... Nature.com Accurate determination of protein structure by NMR spectroscopy is challenging for larger proteins, for which experimental data are often incomplete and ambiguous. Evolutionary sequence information together with advances in...	nmrlearner	Online News	0	10-25-2015 07:39 AM
Protein structure determination by combining sparse NMR data with evolutionary ... - Nature.com Protein structure determination by combining sparse NMR data with evolutionary ... - Nature.com http://www.bionmr.com//t2.gstatic.com/images?q=tbn:ANd9GcRAVMjcYJ2gxDPN-3Oth6tCSQX0HVph0fL6VLvmc9MUU9DwEpS7_iPfM2J5zIur2nI7-EtteAI Nature.com <img alt="" height="1" width="1"> Protein structure determination by combining sparse NMR data with evolutionary ... Nature.com Accurate determination of protein structure by NMR spectroscopy is challenging for larger proteins, for which experimental data are often incomplete and ambiguous. Evolutionary sequence information together with advances in...	nmrlearner	Online News	0	07-10-2015 04:22 PM
[NMR paper] Protein structure determination by combining sparse NMR data with evolutionary couplings. Protein structure determination by combining sparse NMR data with evolutionary couplings. Protein structure determination by combining sparse NMR data with evolutionary couplings. Nat Methods. 2015 Jun 29; Authors: Tang Y, Huang YJ, Hopf TA, Sander C, Marks DS, Montelione GT Abstract Accurate determination of protein structure by NMR spectroscopy is challenging for larger proteins, for which experimental data are often incomplete and ambiguous. Evolutionary sequence information together with advances in maximum entropy...	nmrlearner	Journal club	0	06-30-2015 11:41 AM
Protein structure determination by combining sparse NMR data with evolutionary ... - Nature.com Protein structure determination by combining sparse NMR data with evolutionary ... - Nature.com http://www.bionmr.com//t2.gstatic.com/images?q=tbn:ANd9GcRAVMjcYJ2gxDPN-3Oth6tCSQX0HVph0fL6VLvmc9MUU9DwEpS7_iPfM2J5zIur2nI7-EtteAI Nature.com <img alt="" height="1" width="1"> Protein structure determination by combining sparse NMR data with evolutionary ... Nature.com Accurate determination of protein structure by NMR spectroscopy is challenging for larger proteins, for which experimental data are often incomplete and ambiguous. Evolutionary sequence information together with advances in...	nmrlearner	Online News	0	06-29-2015 07:21 PM
Introduction to protein structure from sparse data Introduction to protein structure from sparse data Introduction to protein structure determination from sparse experimental data More...	nmrlearner	General	0	10-21-2012 06:59 AM
Humans, aliens, and eHarmony or why there is no such thing as a free lunch in protein structure determination from sparse experimental data <img src="http://images.slidesharecdn.com/groupmeetingpresentations72712fcut4-120820213018-phpapp01/95/slide-1-728.jpg?1345517350" width=60%> Downloads: A new file has been added by markber: Protein_structure_determination_from_sparse_data Watch online Humans, aliens, and eHarmony or why there is no such thing as a free lunch in protein structure determination from sparse experimental data	markber	NMR presentations	0	08-21-2012 02:19 AM
[NMR paper] TOUCHSTONEX: protein structure prediction with sparse NMR data. TOUCHSTONEX: protein structure prediction with sparse NMR data. Related Articles TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins. 2003 Nov 1;53(2):290-306 Authors: Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione GT, Kolinski A, Skolnick J TOUCHSTONEX, a new method for folding proteins that uses a small number of long-range contact restraints derived from NMR experimental NOE (nuclear Overhauser enhancement) data, is described. The method employs a new lattice-based, reduced model of proteins that explicitly...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
[NMR paper] De novo protein structure determination using sparse NMR data. De novo protein structure determination using sparse NMR data. Related Articles De novo protein structure determination using sparse NMR data. J Biomol NMR. 2000 Dec;18(4):311-8 Authors: Bowers PM, Strauss CE, Baker D We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models...	nmrlearner	Journal club	0	11-19-2010 08:29 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