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 07-14-2021, 10:07 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 21,280
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 Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration

Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration

The YTH domain of YTHDC1 belongs to a class of protein "readers", recognizing the N6-methyladenosine (m?A) chemical modification in mRNA. Static ensemble-averaged structures revealed details of N6-methyl recognition via a conserved aromatic cage. Here, we performed molecular dynamics (MD) simulations along with nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) to examine how dynamics and solvent interactions contribute to the m?A recognition and negative selectivity...

More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations.
Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations. Related Articles Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations. PLoS One. 2017;12(3):e0174337 Authors: Bomblies R, Luitz MP, Scanu S, Madl T, Zacharias M Abstract Many natural proteins are, as a whole or in part, intrinsically disordered. Frequently, such intrinsically disordered regions (IDRs) undergo a transition to a defined and often...
nmrlearner Journal club 0 03-30-2017 06:42 PM
[NMR paper] Protein-Carbohydrate Interactions Studied by NMR. from Molecular Recognition to Drug Design.
Protein-Carbohydrate Interactions Studied by NMR. from Molecular Recognition to Drug Design. Related Articles Protein-Carbohydrate Interactions Studied by NMR. from Molecular Recognition to Drug Design. Curr Protein Pept Sci. 2012 Dec 10; Authors: Fernandez-Alonso MD, Diaz D, Berbis MA, Marcelo F, Jimenez-Barbero J Abstract Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of...
nmrlearner Journal club 0 02-03-2013 10:22 AM
Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle studied by circular dichroism, NMR spectroscopy and molecular dynamics.
Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle studied by circular dichroism, NMR spectroscopy and molecular dynamics. Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle studied by circular dichroism, NMR spectroscopy and molecular dynamics. Biochim Biophys Acta. 2011 Sep;1808(9):2102-10 Authors: Anselmi M, Eliseo T, Zanetti-Polzi L, Fullone MR, Fogliano V, Di Nola A, Paci M, Grgurina I Abstract Syringomycin E (SRE) is a member of a...
nmrlearner Journal club 0 09-13-2011 08:27 PM
[NMR paper] The hydration of amides in helices; a comprehensive picture from molecular dynamics,
The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR. Related Articles The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR. Protein Sci. 2003 Mar;12(3):520-31 Authors: Walsh ST, Cheng RP, Wright WW, Alonso DO, Daggett V, Vanderkooi JM, DeGrado WF We examined the hydration of amides of alpha(3)D, a simple, designed three-helix bundle protein. Molecular dynamics calculations show that the amide carbonyls on the surface of the protein tilt away from the...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex.
NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex. Related Articles NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex. J Mol Biol. 2000 Oct 6;302(5):1101-17 Authors: Tsui V, Radhakrishnan I, Wright PE, Case DA The hydration of a high-affinity protein-DNA complex involving the three amino terminal zinc finger domains of transcription factor IIIA (TFIIIA) and a 15-base-pair DNA duplex was investigated by NMR spectroscopy and molecular dynamics (MD) simulations. Intermolecular nuclear...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy.
Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy. Related Articles Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy. Biochemistry. 1995 Dec 26;34(51):16608-17 Authors: Broadhurst RW, Hardman CH, Thomas JO, Laue ED The HMG-box sequence motif (approximately 80 residues) occurs in a number of abundant eukaryotic chromosomal proteins such as HMG1, which binds DNA without sequence specificity, but with "structure specificity", as well as in several sequence-specific transcription factors. HMG1...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the cas
Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin. Biophys J. 1999 May;76(5):2390-411 Authors: ...
nmrlearner Journal club 0 08-21-2010 04:03 PM
The Role of Basic Amino Acids in the Molecular Recognition of Hydroxyapatite by Stath
The Role of Basic Amino Acids in the Molecular Recognition of Hydroxyapatite by Statherin using Solid State NMR. Related Articles The Role of Basic Amino Acids in the Molecular Recognition of Hydroxyapatite by Statherin using Solid State NMR. Surf Sci. 2010 Aug 15;604(15-16):L39-L42 Authors: Ndao M, Ash JT, Stayton PS, Drobny GP Organisms use proteins such as statherin to control the growth of hydroxyapatite (HAP), which is the principal component of teeth and bone. Though much emphasis has been placed on the acidic character of these...
nmrlearner Journal club 0 08-17-2010 03:36 AM


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 - 2021, 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 09:31 PM.


Map