NMR paper Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

		BioNMR > Educational resources > Journal club
[NMR paper] Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

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

08-12-2015, 10:04 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,733

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

Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

Related Articles Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

J Bioinform Comput Biol. 2015 Jun 24;:1550020

Authors: Akhmedov M, Çatay B, Apayd?n MS

Abstract
Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to corresponding amino acids, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this problem using a template structure that is homologous to the target. Our previously developed approach Nuclear Vector Replacement-Binary Integer Programming (NVR-BIP) computed the optimal solution for small proteins, but was unable to solve the assignments of large proteins. NVR-Ant Colony Optimization (ACO) extended the applicability of the NVR approach for such proteins. One of the input data utilized in these approaches is the Nuclear Overhauser Effect (NOE) data. NOE is an interaction observed between two protons if the protons are located close in space. These protons could be amide protons, protons attached to the alpha-carbon atom in the backbone of the protein, or side chain protons. NVR only uses backbone protons. In this paper, we reformulate the NVR-BIP model to distinguish the type of proton in NOE data and use the corresponding proton coordinates in the extended formulation. In addition, the threshold value over interproton distances is set in a standard manner for all proteins by extracting the NOE upper bound distance information from the data. We also convert NOE intensities into distance thresholds. Our new approach thus handles the NOE data correctly and without manually determined parameters. We accordingly adapt NVR-ACO solution methodology to these changes. Computational results show that our approaches obtain optimal solutions for small proteins. For the large proteins our ant colony optimization-based approach obtains promising results.

PMID: 26260854 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15 N or 13 Câ?² chemical shifts of multiple contiguous residues in highly resolved 3D spectra Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15 N or 13 Câ?² chemical shifts of multiple contiguous residues in highly resolved 3D spectra Abstract Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings...	nmrlearner	Journal club	0	01-12-2015 11:31 PM
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction Abstract A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential \(^{1}\hbox {H}\) data acquisition for moderately sized proteins is presented. The suitability of the approach for obtaining sequential resonance assignments, including complete ...	nmrlearner	Journal club	0	06-19-2014 10:21 PM
[Question from NMRWiki Q&A forum] what is hard and soft pulse and its usage what is hard and soft pulse and its usage what is hard and soft pulse and its usage Check if somebody has answered this question on NMRWiki QA forum	nmrlearner	News from other NMR forums	0	04-24-2013 09:48 PM
GeNMR - template-based structure generation from NMR data GeNMR website GeNMR (GEnerate NMR structures) is a web server for template-based or ab initio generation of 3D protein structures using NOE-derived distance restraints and NMR chemical shifts. The web server produces an ensemble of PDB coordinates within a period ranging from 20 minutes to 4 hours, depending on protein size, server load, quality and type of experimental information, and selected protocol options. References: 1. Berjanskii M, Tang P, Liang J, Cruz JA, Zhou J, Zhou Y, Bassett E, MacDonell C, Lu P, Lin G, Wishart DS. (2009)GeNMR: a web server for rapid NMR-based...	markber	NMR software	0	02-23-2012 10:21 PM
Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy. Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy. Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy. J Am Chem Soc. 2011 Mar 24; Authors: Linser R, Bardiaux B, Higman V, Fink U, Reif B Magic-angle spinning (MAS) solid-state NMR becomes an increasingly important tool for the determination of structures of membrane...	nmrlearner	Journal club	0	03-26-2011 07:00 PM
Structure Calculation from Unambiguous Long-Range Amide and Methyl 1H-1H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy Structure Calculation from Unambiguous Long-Range Amide and Methyl 1H-1H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy Rasmus Linser, Benjamin Bardiaux, Victoria Higman, Uwe Fink and Bernd Reif http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja110222h/aop/images/medium/ja-2010-10222h_0004.gif Journal of the American Chemical Society DOI: 10.1021/ja110222h http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/Dh0EBf8PwcY	nmrlearner	Journal club	0	03-24-2011 08:02 PM
[NMR paper] A constraint reasoning system for automating sequence-specific resonance assignments A constraint reasoning system for automating sequence-specific resonance assignments from multidimensional protein NMR spectra. Related Articles A constraint reasoning system for automating sequence-specific resonance assignments from multidimensional protein NMR spectra. Proc Int Conf Intell Syst Mol Biol. 1993;1:447-55 Authors: Zimmerman DE, Kulikowski CA, Montelione GT AUTOASSIGN is a prototype expert system designed to aid in the determination of protein structure from nuclear magnetic resonance (NMR) measurements. In this paper we focus...	nmrlearner	Journal club	0	08-21-2010 11:53 PM
Structure-based protein NMR assignments using native structural ensembles Structure-based protein NMR assignments using native structural ensembles Mehmet Serkan Apaydın, Vincent Conitzer and Bruce Randall Donald Journal of Biomolecular NMR; 2008; 40(4); pp 263-276 Abstract: An important step in NMR protein structure determination is the assignment of resonances and NOEs to corresponding nuclei. Structure-based assignment (SBA) uses a model structure (“template”) for the target protein to expedite this process. Nuclear vector replacement (NVR) is an SBA framework that combines multiple sources of NMR data (chemical shifts, RDCs, sparse NOEs, amide exchange...	matthias	Journal club	0	08-14-2008 12:54 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