We present an automated NMR-guided docking workflow that can be used to generate models of protein-ligand complexes based on data from NOE NMR experiments. The first step is to generate a number of intermolecular distance constraints from experimental NOE data. Then, the ligand is docked on an ensemble of receptor structures to account for protein flexibility, and multiple poses are generated. Finally, we use the NOE-based constraints to filter and score docking poses based on the percentage of...
[NMR paper] An NMR-Guided Screening Method for Selective Fragment Docking and Synthesis of a Warhead Inhibitor.
An NMR-Guided Screening Method for Selective Fragment Docking and Synthesis of a Warhead Inhibitor.
Related Articles An NMR-Guided Screening Method for Selective Fragment Docking and Synthesis of a Warhead Inhibitor.
Molecules. 2016;21(7)
Authors: Khattri RB, Morris DL, Davis CM, Bilinovich SM, Caras AJ, Panzner MJ, Debord MA, Leeper TC
Abstract
Selective hits for the glutaredoxin ortholog of Brucella melitensis are determined using STD NMR and verified by trNOE and (15)N-HSQC titration. The most promising hit, RK207, was...
nmrlearner
Journal club
0
07-22-2016 01:34 AM
[NMR paper] NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
J Biomol NMR. 2015 Mar 4;
Authors: Jang R, Wang Y, Xue Z, Zhang Y
Abstract
NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second...
nmrlearner
Journal club
0
03-06-2015 12:45 AM
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment
Abstract
NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements....
nmrlearner
Journal club
0
03-04-2015 08:56 AM
[NMR paper] Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking.
Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acs_authorchoice.jpg http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking.
Biochemistry. 2014 Oct 28;53(42):6706-16
Authors: Ferguson FM, Dias DM, Rodrigues JP, Wienk H, Boelens R,...
nmrlearner
Journal club
0
12-17-2014 09:43 PM
Binding Hotspots of BAZ2B Bromodomain: Histone InteractionRevealed by Solution NMR Driven Docking
Binding Hotspots of BAZ2B Bromodomain: Histone InteractionRevealed by Solution NMR Driven Docking
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi500909d/20141015/images/medium/bi-2014-00909d_0011.gif
Biochemistry
DOI: 10.1021/bi500909d
http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/bichaw/~4/VdojweDGLHw
More...
nmrlearner
Journal club
0
10-16-2014 12:12 AM
[NMR paper] Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
Related Articles Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
Proteins. 2005 Aug 15;60(3):367-81
Authors: van Dijk AD, Fushman D, Bonvin AM
When classical, Nuclear Overhauser Effect (NOE)-based approaches fail, it is possible, given high-resolution...
nmrlearner
Journal club
0
12-01-2010 06:56 PM
[NMR paper] A novel approach for assessing macromolecular complexes combining soft-docking calcul
A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
Related Articles A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
Protein Sci. 2001 Oct;10(10):2131-7
Authors: Morelli XJ, Palma PN, Guerlesquin F, Rigby AC
We present a novel and efficient approach for assessing protein-protein complex formation, which combines ab initio docking calculations performed with the protein docking algorithm BiGGER and chemical shift perturbation data...
nmrlearner
Journal club
0
11-19-2010 08:44 PM
[NMR paper] NMR-restrained docking of a peptidic inhibitor to the N-terminal domain of the phosph
NMR-restrained docking of a peptidic inhibitor to the N-terminal domain of the phosphoenolpyruvate:sugar phosphotransferase enzyme I.
Related Articles NMR-restrained docking of a peptidic inhibitor to the N-terminal domain of the phosphoenolpyruvate:sugar phosphotransferase enzyme I.
J Comput Aided Mol Des. 2001 Feb;15(2):103-15
Authors: Rognan D, Mukhija S, Folkers G, Zerbe O
Starting from the NMR structure of the binary complex between the N-terminal domain of the unphosphorylated enzyme I (EIN) of the phosphoenolpyruvate:sugar...
NMR Data-Driven Docking of HDM2-Inhibitor Complexes
Linear Mode
