NMR paper DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles.

		BioNMR > Educational resources > Journal club
[NMR paper] DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles.

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

01-24-2021, 11:14 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

DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles.

Related Articles DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles.

PLoS Comput Biol. 2021 Jan 22;17(1):e1008551

Authors: Tesei G, Martins JM, Kunze MBA, Wang Y, Crehuet R, Lindorff-Larsen K

Abstract
Owing to their plasticity, intrinsically disordered and multidomain proteins require descriptions based on multiple conformations, thus calling for techniques and analysis tools that are capable of dealing with conformational ensembles rather than a single protein structure. Here, we introduce DEER-PREdict, a software program to predict Double Electron-Electron Resonance distance distributions as well as Paramagnetic Relaxation Enhancement rates from ensembles of protein conformations. DEER-PREdict uses an established rotamer library approach to describe the paramagnetic probes which are bound covalently to the protein.DEER-PREdict has been designed to operate efficiently on large conformational ensembles, such as those generated by molecular dynamics simulation, to facilitate the validation or refinement of molecular models as well as the interpretation of experimental data. The performance and accuracy of the software is demonstrated with experimentally characterized protein systems: HIV-1 protease, T4 Lysozyme and Acyl-CoA-binding protein. DEER-PREdict is open source (GPLv3) and available at github.com/KULL-Centre/DEERpredict and as a Python PyPI package pypi.org/project/DEERPREdict.

PMID: 33481784 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase. Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase. Related Articles Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase. ChemMedChem. 2016 Jan 25; Authors: Seetaha S, Yagi-Utsumi M, Yamaguchi T, Ishii K, Hannongbua S, Choowongkomon K, Kato K Abstract Paramagnetism-assisted nuclear magnetic resonance (NMR) techniques can provide long-range structural information...	nmrlearner	Journal club	0	01-26-2016 03:40 PM
[NMR paper] Lipid dynamics studied by calculation of 31P solid-state NMR spectra using ensembles from molecular dynamics simulations. Lipid dynamics studied by calculation of 31P solid-state NMR spectra using ensembles from molecular dynamics simulations. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Lipid dynamics studied by calculation of 31P solid-state NMR spectra using ensembles from molecular dynamics simulations. J Phys Chem B. 2014 May 15;118(19):5119-29 Authors: Hansen SK, Vestergaard M, Thøgersen L, Schiøtt B, Nielsen NC, Vosegaard T Abstract We present a method to...	nmrlearner	Journal club	0	04-22-2015 03:33 PM
[NMR paper] Efficient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination. Efficient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination. Related Articles Efficient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination. Protein Cell. 2013 Nov 27; Authors: Wu K, Shi C, Li J, Wang H, Shi P, Chen L, Wu F, Xiong Y, Tian C PMID: 24282082	nmrlearner	Journal club	0	11-28-2013 05:18 PM
[NMR tweet] NMR Data-Acquisition Software: Agilent introduced the latest version of its data-acquisition software for nuclear magnetic resonance ... NMR Data-Acquisition Software: Agilent introduced the latest version of its data-acquisition software for nuclear magnetic resonance ... Published by davidp98 (David P.) on 2013-04-16T05:52:41Z Source: Twitter	nmrlearner	Twitter NMR	0	04-16-2013 06:22 AM
DEER-Stitch: Combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data DEER-Stitch: Combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data Publication year: 2012 Source:Journal of Magnetic Resonance</br> J.E. Lovett, B.W. Lovett, J. Harmer</br> Over approximately the last fifteen years the electron paramagnetic resonance (EPR) technique of double electron electron resonance (DEER) has attracted considerable attention since it allows for the precise measurement of the dipole-dipole coupling between radicals and thus can lead to distance information between pairs of radicals separated by up to ca. 8 nm....	nmrlearner	Journal club	0	08-22-2012 02:13 AM
Orientation Selective DEER Measurements on Vinculin Tail at X-Band Frequencies Reveal Spin Label Orientations Orientation Selective DEER Measurements on Vinculin Tail at X-Band Frequencies Reveal Spin Label Orientations Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 8 January 2012</br> ChristophAbé, DanielKlose, FranziskaDietrich, Wolfgang H.Ziegler, Yevhen*Polyhach, ...</br> Double electron electron resonance (DEER) spectroscopy has been established as a valuable method to determine distances between spin labels bound to protein molecules. Caused by selective excitation of molecular orientations DEER primary data also depend on the mutual orientation of...	nmrlearner	Journal club	0	01-10-2012 03:38 PM
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and Î¼s motion of proteins relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and Î¼s motion of proteins Abstract Investigation of protein dynamics on the ps-ns and Î¼s-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was...	nmrlearner	Journal club	0	06-06-2011 12:53 AM
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins. relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins. relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins. J Biomol NMR. 2011 May 27; Authors: Bieri M, d'Auvergne EJ, Gooley PR Investigation of protein dynamics on the ps-ns and ?s-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying...	nmrlearner	Journal club	0	05-28-2011 06:50 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