NMR paper PINE-SPARKY.2 for automated NMR-based protein structure research.

		BioNMR > Educational resources > Journal club
[NMR paper] PINE-SPARKY.2 for automated NMR-based protein structure research.

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

12-29-2017, 02:19 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

PINE-SPARKY.2 for automated NMR-based protein structure research.

PINE-SPARKY.2 for automated NMR-based protein structure research.

Related Articles PINE-SPARKY.2 for automated NMR-based protein structure research.

Bioinformatics. 2017 Dec 21;:

Authors: Lee W, Markley JL

Abstract
Summary: NMR (nuclear magnetic resonance) spectroscopy, along with X-ray crystallography and Cryo-EM, is one of the three major tools that enable the determination of atomic-level structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein-ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. The graphical user interface of PINE-SPARKY.2 simplifies chemical shift assignment and verification, automated detection of secondary structural elements, predictions of flexibility and hydrophobic cores, and calculation of three-dimensional structural models.
Availability: PINE-SPARKY.2 is available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org), and to subscribers to the SBGrid (https://sbgrid.org). For a detailed description of the program, see http://www.nmrfam.wisc.edu/pine-sparky2.htm.
Contact: whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.

PMID: 29281006 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] NMR-based automated protein structure determination. NMR-based automated protein structure determination. Related Articles NMR-based automated protein structure determination. Arch Biochem Biophys. 2017 Mar 02;: Authors: Würz JM, Kazemi S, Schmidt E, Bagaria A, Güntert P Abstract NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra,...	nmrlearner	Journal club	0	03-07-2017 08:54 PM
NMR-based automated protein structure determination NMR-based automated protein structure determination Publication date: Available online 2 March 2017 Source:Archives of Biochemistry and Biophysics</br> Author(s): Julia M. Würz, Sina Kazemi, Elena Schmidt, Anurag Bagaria, Peter Güntert</br> NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific...	nmrlearner	Journal club	0	03-03-2017 08:13 AM
[NMR paper] Automated assignment of NMR chemical shifts based on a known structure and 4D spectra. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Automated assignment of NMR chemical shifts based on a known structure and 4D spectra. J Biomol NMR. 2016 Aug 2; Authors: Trautwein M, Fredriksson K, Möller HM, Exner TE Abstract Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is...	nmrlearner	Journal club	0	08-04-2016 11:21 PM
Automated assignment of NMR chemical shifts based on a known structure and 4D spectra Automated assignment of NMR chemical shifts based on a known structure and 4D spectra Abstract Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely...	nmrlearner	Journal club	0	08-03-2016 04:58 AM
PONDEROSA-C/S: clientâ??server based software package for automated protein 3D structure determination PONDEROSA-C/S: clientâ??server based software package for automated protein 3D structure determination Abstract Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727â??1728. doi:10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein...	nmrlearner	Journal club	0	09-05-2014 03:03 PM
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
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks. Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks. Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks. J Comput Biol. 2011 Mar;18(3):347-63 Authors: Jang R, Gao X, Li M Abstract In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow...	nmrlearner	Journal club	0	03-10-2011 03:51 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