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 11-08-2017, 02:52 PM
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 Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.

Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.

Related Articles Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.

Comput Theor Chem. 2017 Jan 01;1099:152-166

Authors: Koes DR, Vries JK

Abstract
Accurate chemical shifts for the atoms in molecular mechanics (MD) trajectories can be obtained from quantum mechanical (QM) calculations that depend solely on the coordinates of the atoms in the localized regions surrounding atoms of interest. If these coordinates are correct and the sample size is adequate, the ensemble average of these chemical shifts should be equal to the chemical shifts obtained from NMR spectroscopy. If this is not the case, the coordinates must be incorrect. We have utilized this fact to quantify the errors associated with the backbone atoms in MD simulations of proteins. A library of regional conformers containing 169,499 members was constructed from 6 model proteins. The chemical shifts associated with the backbone atoms in each of these conformers was obtained from QM calculations using density functional theory at the B3LYP level with a 6-311+G(2d,p) basis set. Chemical shifts were assigned to each backbone atom in each MD simulation frame using a template matching approach. The ensemble average of these chemical shifts was compared to chemical shifts from NMR spectroscopy. A large systematic error was identified that affected the (1)H atoms of the peptide bonds involved in hydrogen bonding with water molecules or peptide backbone atoms. This error was highly sensitive to changes in electrostatic parameters. Smaller errors affecting the (13)C(a) and (15)N atoms were also detected. We believe these errors could be useful as metrics for comparing the force-fields and parameter sets used in MD simulation because they are directly tied to errors in atomic coordinates.


PMID: 29109930 [PubMed]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Evaluating Amber force fields using computed NMR chemical shifts.
Evaluating Amber force fields using computed NMR chemical shifts. Related Articles Evaluating Amber force fields using computed NMR chemical shifts. Proteins. 2017 Jul 08;: Authors: Koes DR, Vries JK Abstract NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations....
nmrlearner Journal club 0 07-09-2017 11:44 PM
[NMR paper] CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.
CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. Related Articles CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. J Phys Chem B. 2017 Feb 09;: Authors: Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P Abstract Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many...
nmrlearner Journal club 0 02-10-2017 04:19 PM
[NMR paper] NMR Order Parameter Determination from Long Molecular Dynamics Trajectories for Objective Comparison with Experiment.
NMR Order Parameter Determination from Long Molecular Dynamics Trajectories for Objective Comparison with Experiment. Related Articles NMR Order Parameter Determination from Long Molecular Dynamics Trajectories for Objective Comparison with Experiment. J Chem Theory Comput. 2014 Jun 10;10(6):2599-607 Authors: Gu Y, Li DW, Brüschweiler R Abstract Functional protein motions covering a wide range of time scales can be studied, among other techniques, by NMR and by molecular dynamics (MD) computer simulations. MD simulations of...
nmrlearner Journal club 0 11-22-2015 01:36 AM
[NMR paper] Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins. J Phys Chem B. 2013 Feb 1; Authors: Camilloni C, Cavalli A, Vendruscolo M Abstract It has been recently...
nmrlearner Journal club 0 02-03-2013 10:19 AM
Rotational velocity rescaling of molecular dynamics trajectories for direct prediction of protein NMR relaxation
Rotational velocity rescaling of molecular dynamics trajectories for direct prediction of protein NMR relaxation July 2012 Publication year: 2012 Source:Biophysical Chemistry, Volumes 168–169</br> </br> Rotational velocity rescaling (RVR) enables 15N relaxation data for the anisotropically tumbling B3 domain of Protein G (GB3) to be accurately predicted from 1?s of constant energy molecular dynamics simulation without recourse to any system-specific adjustable parameters. Superposition of adjacent trajectory frames yields the unique rotation axis and angle of rotation...
nmrlearner Journal club 0 02-03-2013 10:13 AM
[NMR paper] The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine p
The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine pancreatic trypsin inhibitor dynamics in water as a test case for solvent influences. Related Articles The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine pancreatic trypsin inhibitor dynamics in water as a test case for solvent influences. J Pept Sci. 2003 Jul;9(7):450-60 Authors: Busetta B, Picard P, Precigoux G In this paper the NMR secondary chemical shifts, that are estimated from a set of 3D-structures, are compared with...
nmrlearner Journal club 0 11-24-2010 09:16 PM
Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations
Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins. Related Articles Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins. Structure. 2010 Aug 11;18(8):923-933 Authors: Robustelli P, Kohlhoff K, Cavalli A, Vendruscolo M We introduce a procedure to determine the structures of proteins by incorporating NMR chemical shifts as structural restraints in molecular dynamics simulations. In this approach, the chemical shifts are expressed as differentiable...
nmrlearner Journal club 0 08-17-2010 03:36 AM
Sequential nearest-neighbor effects on computed 13Cα chemical shifts
Abstract To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of 13Cα chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue α/β protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed 13Cα chemical...
nmrlearner Journal club 0 08-14-2010 04:19 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 11:00 AM.


Map