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 09-06-2011, 08:17 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 Generative probabilistic models extend the scope of inferential structure determination

Generative probabilistic models extend the scope of inferential structure determination


Publication year: 2011
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 6 September 2011

Simon, Olsson , Wouter, Boomsma , Jes, Frellsen , Sandro, Bottaro , Tim, Harder , ...

Conventional methods for protein structure determination from NMR data rely on the ad hoc combination of physical forcefields and experimental data, along with heuristic determination of free parameters such as weight of experimental data relative to a physical forcefield. Recently, a theoretically rigorous approach was developed which treats structure determination as a problem of Bayesian inference. In this case, the forcefields are brought in as a prior distribution in the form of a Boltzmann factor. Due to high computational cost, the approach has been only sparsely applied in practice. Here, we demonstrate that the use of generative probabilistic models instead...

Graphical abstract

*Graphical abstract:**Highlights:*? Generative probabilistic models in inferential structure determination are examined. ? We observe increased efficiency and precision compared to previous studies. ? The scope of inferential structure determination has been extended to practioners. ? The scope of inferential structure determination has been extended to practioners.




Source: Journal of Magnetic Resonance
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Post-doc position on Validation of Low-resolution Models
Post-doc position on Validation of Low-resolution Models Hi all, There is an EMBL Inter-disciplinary Post-doc (EIPOD) position available to work on "Validation of low resolution structural models". For details, see: More...
nmrlearner Job marketplace 0 01-26-2011 04:27 PM
Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.
Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction. Related Articles Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction. Structure. 2010 Dec 8;18(12):1678-1687 Authors: Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the...
nmrlearner Journal club 0 12-08-2010 06:21 PM
[NMR paper] NMR structure determination and structure-based functional characterization of conser
NMR structure determination and structure-based functional characterization of conserved hypothetical protein MTH1175 from Methanobacterium thermoautotrophicum. Related Articles NMR structure determination and structure-based functional characterization of conserved hypothetical protein MTH1175 from Methanobacterium thermoautotrophicum. J Struct Funct Genomics. 2000;1(1):15-25 Authors: Cort JR, Yee A, Edwards AM, Arrowsmith CH, Kennedy MA The solution structure of MTH1175, a 124-residue protein from the archaeon Methanobacterium...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] Expanding the Scope of Protein Biosynthesis by Altering the Methionyl-tRNA Synthetase
Expanding the Scope of Protein Biosynthesis by Altering the Methionyl-tRNA Synthetase Activity of a Bacterial Expression Host Scott Ross was helpful in conducting the 1D TOCSY NMR experiments and Pratip Bhattachary is thanked for assistance in other NMR experiments. We are grateful to Yves Mechulam for a sample of plasmid pBSM547W305F and to Hieronim Jakubowski of UMDNJ-New Jersey Medical School, Newark, New Jersey, for plasmid pGG3. K.L.K. thanks the U.S. Department of Defense for a National Defense Science and Engineering Graduate Fellowship. This work was supported by grants from the...
nmrlearner Journal club 0 11-18-2010 09:15 PM
(15)N and (13)C Group-Selective Techniques Extend the Scope of STD NMR Detection of W
(15)N and (13)C Group-Selective Techniques Extend the Scope of STD NMR Detection of Weak Host-Guest Interactions and Ligand Screening. Related Articles (15)N and (13)C Group-Selective Techniques Extend the Scope of STD NMR Detection of Weak Host-Guest Interactions and Ligand Screening. Chembiochem. 2010 Sep 28; Authors: Kövér KE, Wéber E, Martinek TA, Monostori E, Batta G Saturation transfer difference (STD) is a valuable tool for studying the binding of small molecules to large biomolecules and for obtaining detailed information on the binding...
nmrlearner Journal club 0 09-30-2010 06:54 PM
Quality of Macromolecular Models
Quality of Macromolecular Models More...
nmrlearner NMR bookmarks 0 08-19-2010 02:34 PM
A probabilistic approach for validating protein NMR chemical shift assignments
Abstract It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program...
nmrlearner Journal club 0 08-14-2010 04:19 AM
Script for impatient: get models from NMR ensemble
Python script for Linux to extract models from an NMR ensemble http://www.istockphoto.com/file_thumbview_approve/257688/2/istockphoto_Mad_Scientist_2_6_257688.jpg Download USAGE: python PDB_model_extractor_1b.py -f name_of_pdb_file -m numbers_of_models
nmrlearner General 0 09-08-2005 09:55 AM


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 - 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 04:47 PM.


Map