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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 02-16-2024, 07:14 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
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 Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data

Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data

ASPP2 and iASPP bind to p53 through their conserved ANK-SH3 domains to respectively promote and inhibit p53-dependent cell apoptosis. While crystallography has indicated that these two proteins employ distinct surfaces of their ANK-SH3 domains to bind to p53, solution NMR data has suggested similar surfaces. In this study, we employed multi-scale molecular dynamics (MD) simulations combined with free energy calculations to reconcile the discrepancy in the binding modes. We demonstrated that the...

More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Binding of Glycans to the SARS CoV-2 Spike Protein, an Open Question: NMR Data on Binding Site Localization, Affinity, and Selectivity
Binding of Glycans to the SARS CoV-2 Spike Protein, an Open Question: NMR Data on Binding Site Localization, Affinity, and Selectivity We have used NMR experiments to explore binding of selected glycans and glycomimetics to the SARS CoV-2 spike glycoprotein (S-protein) and to its receptor binding domain (RBD). STD NMR experiments confirm binding of sialoglycans to the S-protein of the prototypic Wuhan strain virus and yield dissociation constants in the mM range. The absence of STD effects for sialoglycans in the presence of the Omicron/BA.1 S-protein reflects a loss of binding as a result...
nmrlearner Journal club 0 09-27-2022 05:49 AM
[ASAP] Distribution of Aluminum Species in Zeolite Catalysts: 27Al NMR of Framework, Partially-Coordinated Framework, and Non-Framework Moieties
Distribution of Aluminum Species in Zeolite Catalysts: 27Al NMR of Framework, Partially-Coordinated Framework, and Non-Framework Moieties Kuizhi Chen, Zhehong Gan, Sarah Horstmeier, and Jeffery L. White https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.1c02361/20210421/images/medium/ja1c02361_0009.gif Journal of the American Chemical Society DOI: 10.1021/jacs.1c02361 http://feeds.feedburner.com/~r/acs/jacsat/~4/N3AHspUg8Fw
nmrlearner Journal club 0 04-22-2021 11:26 AM
[NMR paper] Analysis of Binding Mode of 2'-GMP to Proteins Using 1H/31P NMR Spectroscopy.
Analysis of Binding Mode of 2'-GMP to Proteins Using 1H/31P NMR Spectroscopy. Related Articles Analysis of Binding Mode of 2'-GMP to Proteins Using 1H/31P NMR Spectroscopy. Anal Sci. 2020 Aug 07;: Authors: Suka N, Okizumi K, Furihata K, Tashiro M PMID: 32779575
nmrlearner Journal club 0 08-12-2020 02:10 PM
[NMR paper] Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography.
Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.nature.com-images-lo_npg.gif http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--www.ncbi.nlm.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.png Related Articles Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography. Nat Commun. 2019 02 07;10(1):638 Authors: Chen S, Lu M, Liu D, Yang L, Yi C, Ma L, Zhang H, Liu Q,...
nmrlearner Journal club 0 04-09-2019 11:33 PM
Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets
Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets Wan-Na Chen, Christoph Nitsche, Kala Bharath Pilla, Bim Graham, Thomas Huber, Christian D. Klein and Gottfried Otting http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.6b00416/20160324/images/medium/ja-2016-004167_0006.gif Journal of the American Chemical Society DOI: 10.1021/jacs.6b00416 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/yfHNdUxBP5M
nmrlearner Journal club 0 03-25-2016 04:12 PM
[NMR paper] Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets.
Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets. Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets. J Am Chem Soc. 2016 Mar 14; Authors: Chen WN, Nitsche C, Pilla KB, Graham B, Huber T, Klein CD, Otting G Abstract Structure-guided drug design relies on detailed structural knowledge of protein-ligand complexes, but crystallization of co-complexes is not always possible. Here we present a sensitive nuclear...
nmrlearner Journal club 0 03-15-2016 11:57 AM
[NMR paper] Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations.
Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations. Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations. PLoS One. 2013;8(9):e74040 Authors: Huan X, Shi J, Lim L, Mitra S, Zhu W, Qin H, Pasquale EB, Song J Abstract The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions...
nmrlearner Journal club 0 10-03-2013 03:31 PM
NMR Reveals a Different Mode of Binding of the Stam2 VHS Domain to Ubiquitin and Diubiquitin,
NMR Reveals a Different Mode of Binding of the Stam2 VHS Domain to Ubiquitin and Diubiquitin, http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi101594a/aop/images/medium/bi-2010-01594a_0006.gif Biochemistry DOI: 10.1021/bi101594a http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/HJPaBUvhJsw More...
nmrlearner Journal club 0 12-15-2010 12:16 AM



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 02:18 PM.


Map