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 06-06-2018, 01:42 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 18,793
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 Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.

Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.

Related Articles Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.

Front Chem. 2018;6:150

Authors: Jin X, Zhu T, Zhang JZH, He X

Abstract
In this study, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method was applied for NMR chemical shift calculations of protein-ligand complexes. In the AF-QM/MM approach, the protein binding pocket is automatically divided into capped fragments (within ~200 atoms) for density functional theory (DFT) calculations of NMR chemical shifts. Meanwhile, the solvent effect was also included using the Poission-Boltzmann (PB) model, which properly accounts for the electrostatic polarization effect from the solvent for protein-ligand complexes. The NMR chemical shifts of neocarzinostatin (NCS)-chromophore binding complex calculated by AF-QM/MM accurately reproduce the large-sized system results. The 1H chemical shift perturbations (CSP) between apo-NCS and holo-NCS predicted by AF-QM/MM are also in excellent agreement with experimental results. Furthermore, the DFT calculated chemical shifts of the chromophore and residues in the NCS binding pocket can be utilized as molecular probes to identify the correct ligand binding conformation. By combining the CSP of the atoms in the binding pocket with the Glide scoring function, the new scoring function can accurately distinguish the native ligand pose from decoy structures. Therefore, the AF-QM/MM approach provides an accurate and efficient platform for protein-ligand binding structure prediction based on NMR derived information.


PMID: 29868556 [PubMed]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Calculation of 15N NMR chemical shifts: recent advances and perspectives
Calculation of 15N NMR chemical shifts: recent advances and perspectives Publication date: Available online 24 August 2017 Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br> Author(s): Leonid B. Krivdin</br> Recent advances in computation of 15N NMR chemical shifts are reviewed, concentrating mainly on practical aspects of computational protocols and accuracy factors. The review includes the discussion of the level of theory, the choice of density functionals and basis sets together with taking into account solvent effects, rovibrational corrections...
nmrlearner Journal club 0 08-25-2017 05:31 PM
[NMR paper] Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.
Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions. Related Articles Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions. J Chem Theory Comput. 2016 Dec 19; Authors: Steinmann C, Bratholm LA, Olsen JM, Kongsted J Abstract Full-protein NMR shielding constants based on ab initio calculations are desirable since they can assist in...
nmrlearner Journal club 0 12-21-2016 07:20 AM
[NMR paper] AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. Related Articles AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J Biomol NMR. 2015 Aug 2; Authors: Swails J, Zhu T, He X, Case DA Abstract We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects...
nmrlearner Journal club 0 08-04-2015 03:00 PM
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules Abstract We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poissonâ??Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation...
nmrlearner Journal club 0 08-02-2015 07:10 AM
Automated Method for Purifying Protein:Ligand Complexes - News-Medical.net
Automated Method for Purifying Protein:Ligand Complexes - News-Medical.net http://www.bionmr.com//t1.gstatic.com/images?q=tbn:ANd9GcQutdD6NnjJDnC9but3zjmMB4bBDLXFw5LX7xJfJWUzs2t8oAX-oS63Npooi2n9ra6w4V88Fp8j News-Medical.net <img alt="" height="1" width="1"> Automated Method for Purifying Protein:Ligand Complexes News-Medical.net Common techniques for further analyzing protein:ligand complexes to gain structural information include X-ray crystallography, NMR, and cryo-EM. However, a lack of reproducible and robust separation techniques means the purification of protein:ligand ...
nmrlearner Online News 0 05-20-2015 10:27 AM
[NMR paper] Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method. Related Articles Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method. Adv Exp Med Biol. 2015;827:49-70 Authors: Zhu T, Zhang JZ, He X Abstract The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the...
nmrlearner Journal club 0 11-14-2014 08:33 AM
[NMR paper] NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding.
NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding. Related Articles NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding. Phys Chem Chem Phys. 2014 Mar 7; Authors: Cembran A, Kim J, Gao J, Veglia G Abstract Proteins exist as an ensemble of conformers that are distributed on free energy landscapes resembling folding funnels. While the most stable conformers populate low energy basins, protein function is often...
nmrlearner Journal club 0 03-10-2014 10:35 AM
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 - 2018, 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 02:23 PM.


Map