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.
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:
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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...
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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...
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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...
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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...
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...
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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
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USAGE:
python PDB_model_extractor_1b.py -f name_of_pdb_file -m numbers_of_models
Generative probabilistic models extend the scope of inferential structure determination
Linear Mode
