Protein structure determination by combining sparse NMR data with evolutionary ... - Nature.com

		BioNMR > NMR community > Online News
Protein structure determination by combining sparse NMR data with evolutionary ... - Nature.com

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

06-29-2015, 07:21 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

Protein structure determination by combining sparse NMR data with evolutionary ... - Nature.com

Protein structure determination by combining sparse NMR data with evolutionary ... - Nature.com

Nature.com

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 maximum entropy statistical ...

Read here

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
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
Protein structure modeling using sparse NMR data [Biophysics and Computational Biology] Protein structure modeling using sparse NMR data Thompson, J. M., Sgourakis, N. G., Liu, G., Rossi, P., Tang, Y., Mills, J. L., Szyperski, T., Montelione, G. T., Baker, D.... Date: 2012-06-19 While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that...	nmrlearner	Journal club	0	06-20-2012 02:28 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
[NMR paper] A branch and bound algorithm for protein structure refinement from sparse NMR data se A branch and bound algorithm for protein structure refinement from sparse NMR data sets. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles A branch and bound algorithm for protein structure refinement from sparse NMR data sets. J Mol Biol. 1999 Jan 29;285(4):1691-710 Authors: Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE We describe new methods for predicting protein tertiary structures to low resolution given the specification of secondary structure and a...	nmrlearner	Journal club	0	08-21-2010 04:03 PM
Combining NMR and EPR Methods for Homodimer Protein Structure Determination. Combining NMR and EPR Methods for Homodimer Protein Structure Determination. Related Articles Combining NMR and EPR Methods for Homodimer Protein Structure Determination. J Am Chem Soc. 2010 Aug 10; Authors: Yang Y, Ramelot TA, McCarrick RM, Ni S, Feldmann EA, Cort JR, Wang H, Ciccosanti C, Jiang M, Janjua H, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using...	nmrlearner	Journal club	0	08-17-2010 03:36 AM
Combining NMR and EPR Methods for Homodimer Protein Structure Determination http://pubs.acs.org//appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja105080h/aop/images/medium/ja-2010-05080h_0003.gif Combining NMR and EPR Methods for Homodimer Protein Structure Determination There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein ...	nmrlearner	Journal club	0	08-14-2010 05:56 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 On Trackbacks are Off Pingbacks are Off Refbacks are Off