NMR paper Application of neural networks to automated assignment of NMR spectra of proteins.

		BioNMR > Educational resources > Journal club
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.

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

08-22-2010, 03:33 AM

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

Application of neural networks to automated assignment of NMR spectra of proteins.

Application of neural networks to automated assignment of NMR spectra of proteins.

Related Articles Application of neural networks to automated assignment of NMR spectra of proteins.

J Biomol NMR. 1994 Jan;4(1):35-46

Authors: Hare BJ, Prestegard JH

Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37% sequence homology with E. coli ACP and a similar secondary structure. The output unit corresponding to the correct amino acid is one of the four most activated units in 83% of the spin systems tested. The utility of this information is illustrated by a second network which uses a constraint satisfaction algorithm to find the best fit of the spin systems to the amino acid sequence. Application to a stretch of 20 amino acids in spinach ACP results in 75% correct sequential assignment. Since the output of the amino acid type identification network can be coupled with a variety of sequential assignment strategies, the approach offers substantial potential for expediting assignment of protein NMR spectra.

PMID: 8130640 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Exclusively NOESY-based automated NMR assignment and structure determination of proteins Exclusively NOESY-based automated NMR assignment and structure determination of proteins Abstract A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information. Applied to two small proteins, the approach yielded structures that coincided closely with conventionally determined structures. Content Type Journal Article Pages 1-10 DOI 10.1007/s10858-011-9502-8	nmrlearner	Journal club	0	04-01-2011 09:31 PM
Exclusively NOESY-based automated NMR assignment and structure determination of proteins. Exclusively NOESY-based automated NMR assignment and structure determination of proteins. Exclusively NOESY-based automated NMR assignment and structure determination of proteins. J Biomol NMR. 2011 Mar 30; Authors: Ikeya T, Jee JG, Shigemitsu Y, Hamatsu J, Mishima M, Ito Y, Kainosho M, Güntert P A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information....	nmrlearner	Journal club	0	03-31-2011 06:24 PM
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies. Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies. Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies. J Am Chem Soc. 2010 Dec 16; Authors: Gossert AD, Hiller S, Ferna?ndez C The detection and structural characterization of protein-ligand interactions by solution NMR is central to functional biology research as well as to drug discovery. Here we present a robust and highly automated procedure for obtaining the resonance assignments necessary for studies of such...	nmrlearner	Journal club	0	12-18-2010 12:00 PM
[NMR paper] Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). Related Articles Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). J Biomol NMR. 2002 Aug;23(4):271-87 Authors: Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR Automated assignment of NOESY spectra is a prerequisite for automated structure determination of biological macromolecules. With the program KNOWNOE we present a novel, knowledge based approach to this problem. KNOWNOE...	nmrlearner	Journal club	0	11-24-2010 08:58 PM
[NMR paper] RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins. Related Articles RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins. J Biomol NMR. 1999 Sep;15(1):15-26 Authors: Pons JL, Delsuc MA The assignment of the 1H spectrum of a protein or a polypeptide is the prerequisite for advanced NMR studies. We present here an assignment tool based on the artificial neural network technology, which determines the type of the amino acid from the chemical shift values observed in the 1H...	nmrlearner	Journal club	0	11-18-2010 08:31 PM
[NMR paper] Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment. Related Articles Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment. J Chem Inf Comput Sci. 1997 May-Jun;37(3):467-77 Authors: Li KB, Sanctuary BC A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures...	nmrlearner	Journal club	0	08-22-2010 03:31 PM
[NMR paper] Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment. Related Articles Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment. J Chem Inf Comput Sci. 1997 May-Jun;37(3):467-77 Authors: Li KB, Sanctuary BC A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures...	nmrlearner	Journal club	0	08-22-2010 03:03 PM
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins. Application of neural networks to automated assignment of NMR spectra of proteins. Related Articles Application of neural networks to automated assignment of NMR spectra of proteins. J Biomol NMR. 1994 Jan;4(1):35-46 Authors: Hare BJ, Prestegard JH Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...	nmrlearner	Journal club	0	08-22-2010 03:33 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