BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 01-24-2021, 11:14 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,617
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles.

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...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
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> Christoph*Abé, Daniel*Klose, Franziska*Dietrich, 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 μs motion of proteins
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins Abstract Investigation of protein dynamics on the ps-ns and μs-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


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 09:34 AM.


Map