NMR paper Automated analysis of protein NMR assignments using methods from artificial intellige

		BioNMR > Educational resources > Journal club
[NMR paper] Automated analysis of protein NMR assignments using methods from artificial intellige

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, 03:31 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,780

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

Automated analysis of protein NMR assignments using methods from artificial intellige

Automated analysis of protein NMR assignments using methods from artificial intelligence.

Related Articles Automated analysis of protein NMR assignments using methods from artificial intelligence.

J Mol Biol. 1997 Jun 20;269(4):592-610

Authors: Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien C, Powers R, Montelione GT

An expert system for determining resonance assignments from NMR spectra of proteins is described. Given the amino acid sequence, a two-dimensional 15N-1H heteronuclear correlation spectrum and seven to eight three-dimensional triple-resonance NMR spectra for seven proteins, AUTOASSIGN obtained an average of 98% of sequence-specific spin-system assignments with an error rate of less than 0.5%. Execution times on a Sparc 10 workstation varied from 16 seconds for smaller proteins with simple spectra to one to nine minutes for medium size proteins exhibiting numerous extra spin systems attributed to conformational isomerization. AUTOASSIGN combines symbolic constraint satisfaction methods with a domain-specific knowledge base to exploit the logical structure of the sequential assignment problem, the specific features of the various NMR experiments, and the expected chemical shift frequencies of different amino acids. The current implementation specializes in the analysis of data derived from the most sensitive of the currently available triple-resonance experiments. Potential extensions of the system for analysis of additional types of protein NMR data are also discussed.

PMID: 9217263 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] An integrated platform for automated analysis of protein NMR structures. An integrated platform for automated analysis of protein NMR structures. Related Articles An integrated platform for automated analysis of protein NMR structures. Methods Enzymol. 2005;394:111-41 Authors: Huang YJ, Moseley HN, Baran MC, Arrowsmith C, Powers R, Tejero R, Szyperski T, Montelione GT Recent developments provide automated analysis of NMR assignments and three-dimensional (3D) structures of proteins. These approaches are generally applicable to proteins ranging from about 50 to 150 amino acids. In this chapter, we summarize progress...	nmrlearner	Journal club	0	11-24-2010 11:14 PM
[NMR paper] Automated analysis of protein NMR assignments and structures. Automated analysis of protein NMR assignments and structures. Related Articles Automated analysis of protein NMR assignments and structures. Chem Rev. 2004 Aug;104(8):3541-56 Authors: Baran MC, Huang YJ, Moseley HN, Montelione GT	nmrlearner	Journal club	0	11-24-2010 10:01 PM
[NMR paper] Automated protein NMR resonance assignments. Automated protein NMR resonance assignments. Related Articles Automated protein NMR resonance assignments. Proc IEEE Comput Soc Bioinform Conf. 2003;2:197-208 Authors: Wan X, Xu D, Slupsky CM, Lin G NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming,...	nmrlearner	Journal club	0	11-24-2010 09:01 PM
[NMR paper] Automated analysis of NMR assignments and structures for proteins. Automated analysis of NMR assignments and structures for proteins. Related Articles Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol. 1999 Oct;9(5):635-42 Authors: Moseley HN, Montelione GT Recent developments in protein NMR technology have provided spectral data that are highly amenable to analysis by advanced computer software systems. Specific data collection strategies, coupled with these computer programs, allow automated analysis of extensive backbone and sidechain resonance assignments and...	nmrlearner	Journal club	0	11-18-2010 08:31 PM
Automated protein resonance assignments of magic angle spinning solid-state NMR spect Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of Î²1 immunoglobulin binding domain of protein G (GB1) Abstract Magic-angle spinning solid-state NMR (MAS SSNMR) represents a fast developing experimental technique with great potential to provide structural and dynamics information for proteins not amenable to other methods. However, few automated analysis tools are currently available for MAS SSNMR. We present a methodology for automating protein resonance assignments of MAS SSNMR spectral data and its application to experimental peak lists of the...	nmrlearner	Journal club	0	10-15-2010 05:16 PM
Automated protein resonance assignments of magic angle spinning solid-state NMR spect Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of ?1 immunoglobulin binding domain of protein G (GB1). Related Articles Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of ?1 immunoglobulin binding domain of protein G (GB1). J Biomol NMR. 2010 Oct 8; Authors: Moseley HN, Sperling LJ, Rienstra CM Magic-angle spinning solid-state NMR (MAS SSNMR) represents a fast developing experimental technique with great potential to provide structural and dynamics information for...	nmrlearner	Journal club	0	10-12-2010 02:52 PM
[NMR paper] Automated analysis of protein NMR assignments using methods from artificial intellige Automated analysis of protein NMR assignments using methods from artificial intelligence. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol. 1997 Jun 20;269(4):592-610 Authors: Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien C, Powers R, Montelione GT An expert system for determining resonance assignments from NMR spectra of proteins is...	nmrlearner	Journal club	0	08-22-2010 03:03 PM
Structure-oriented methods for protein NMR data analysis Structure-oriented methods for protein NMR data analysis Publication year: 2010 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 3 March 2010</br> Guillermo A., Bermejo , Miguel, Llinás</br> More...	nmrlearner	Journal club	0	08-16-2010 03:50 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