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 07-06-2020, 10:08 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,040
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 Protein-ligand structure determination with the NMR molecular replacement tool, NMR2.

Protein-ligand structure determination with the NMR molecular replacement tool, NMR2.

Related Articles Protein-ligand structure determination with the NMR molecular replacement tool, NMR2.

J Biomol NMR. 2020 Jul 03;:

Authors: Orts J, Riek R

Abstract
We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a protein-ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules. The algorithm used in the NMR Molecular Replacement program has until now not been*described in detail. Here, we present a complete description of the NMR Molecular Replacement implementation as well as several new features that further reduce the time required for structure elucidation.


PMID: 32621003 [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
Proteinâ??ligand structure determination with the NMR molecular replacement tool, N MR 2
Proteinâ??ligand structure determination with the NMR molecular replacement tool, N MR 2 Abstract We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a proteinâ??ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules. The algorithm used in the NMR Molecular Replacement program has until now not beenÂ*described in detail. Here, we present a complete description of the NMR Molecular...
nmrlearner Journal club 0 07-04-2020 03:45 AM
Structure determination of protein-ligand complexes by NMR in solution
Structure determination of protein-ligand complexes by NMR in solution Publication date: Available online 8 February 2018 Source:Methods</br> Author(s): Julien Orts, Alvar D. Gossert</br> In this paper, we discuss methods for determining structures of protein-ligand complexes by NMR in solution. Our discussion is based on small ligands (<2 kDa) as for example drugs, metabolites or oligo-peptides, but most of the considerations also apply to more general cases. In NMR in solution, the kinetics of association and dissociation of the complex – the exchange rate –...
nmrlearner Journal club 0 03-09-2018 09:52 AM
[NMR paper] Structure determination of protein-ligand complexes by NMR in solution.
Structure determination of protein-ligand complexes by NMR in solution. Structure determination of protein-ligand complexes by NMR in solution. Methods. 2018 Feb 07;: Authors: Orts J, Gossert AD Abstract In this paper, we discuss methods for determining structures of protein-ligand complexes by NMR in solution. Our discussion is based on small ligands (< 2 kDa) as for example drugs, metabolites or oligo-peptides, but most of the considerations also apply to more general cases. In NMR in solution, the kinetics of association and...
nmrlearner Journal club 0 02-11-2018 11:50 AM
[NMR paper] NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment.
NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment. NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment. J Am Chem Soc. 2016 Mar 4; Authors: Orts J, Wälti MA, Marsh M, Vera L, Gossert AD, Güntert P, Riek R Abstract Molecular replacement in X-ray crystallography is the prime method for establishing structure-activity relationships of pharmaceutically relevant molecules. Such an approach is not...
nmrlearner Journal club 0 03-05-2016 11:21 AM
[CNS Yahoo group] Molecular replacement
Molecular replacement HI I have MBP fused protein. I got the x-ray data at 3.1 A resolution. I have solved the MBP structure with the MBP as a model. I can see the density More...
nmrlearner News from other NMR forums 0 02-11-2013 08:42 AM
Improved technologies now routinely provide protein NMR structures useful for molecular replacement.
Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Structure. 2011 Jun 8;19(6):757-66 Authors: Mao B, Guan R, Montelione GT Molecular replacement (MR) is widely used for addressing the phase problem in X-ray crystallography. Historically, crystallographers have had limited success using NMR structures as MR search models. Here, we report a comprehensive investigation of the utility of protein NMR...
nmrlearner Journal club 0 06-08-2011 11:30 AM
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Methods Enzymol. 2011;493:241-75 Authors: Ziarek JJ, Peterson FC, Lytle BL, Volkman BF Over the last 15years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like...
nmrlearner Journal club 0 03-05-2011 01:02 PM
Structure Determination of Protein-Ligand Complexes by Transferred Paramagnetic Shifts
Structure Determination of Protein-Ligand Complexes by Transferred Paramagnetic Shifts Michael John, Guido Pintacuda, Ah Young Park, Nicholas E. Dixon, and Gottfried Otting J. Am. Chem. Soc.; 2006; 128(39) pp 12910 - 12916; (Article) Abstract: Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small...
administrator Protein-ligand interactions 1 03-30-2007 03:03 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 - 2020, 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 08:42 AM.


Map