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 07-15-2017, 05:05 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,709
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 Usage of a dataset of NMR resolved protein structures to test aggregation versus solubility prediction algorithms

Usage of a dataset of NMR resolved protein structures to test aggregation versus solubility prediction algorithms

Abstract

There has been an increased interest in computational methods for amyloid and (or) aggregate prediction, due to the prevalence of these aggregates in numerous diseases and their recently discovered functional importance. To evaluate these methods, several datasets have been compiled. Typically, aggregation-prone regions of proteins, which form aggregates or amyloids in vivo, are more than 15 residues long and intrinsically disordered. However, the number of such experimentally established amyloid forming and non-forming sequences are limited, not exceeding one hundred entries in existing databases. In this work, we parsed all available NMR-resolved protein structures from the PDB and assembled a new, sevenfold larger, dataset of unfolded sequences, soluble at high concentrations. We proposed to use these sequences as a negative set for evaluating methods for predicting aggregation in vivo. We also present the results of benchmarking cutting edge tools for the prediction of aggregation versus solubility propensity.




More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Usage of a dataset of NMR resolved protein structures to test aggregation vs. solubility prediction algorithms.
Usage of a dataset of NMR resolved protein structures to test aggregation vs. solubility prediction algorithms. Related Articles Usage of a dataset of NMR resolved protein structures to test aggregation vs. solubility prediction algorithms. Protein Sci. 2017 Jul 07;: Authors: Roche DB, Villain E, Kajava AV Abstract There has been an increased interest in computational methods for amyloid and (or) aggregate prediction, due to the prevalence of these aggregates in numerous diseases and their recently discovered functional...
nmrlearner Journal club 0 07-08-2017 02:54 PM
Usage of a dataset of NMR resolved protein structures to test aggregation vs. solubility prediction algorithms
Usage of a dataset of NMR resolved protein structures to test aggregation vs. solubility prediction algorithms Abstract There has been an increased interest in computational methods for amyloid and (or) aggregate prediction, due to the prevalence of these aggregates in numerous diseases and their recently discovered functional importance. To evaluate these methods, several datasets have been compiled. Typically, aggregation-prone regions of proteins, which form aggregates or amyloids in vivo, are more than 15 residues long and intrinsically disordered. However, the number of such...
nmrlearner Journal club 0 07-07-2017 03:20 PM
[NMR paper] Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.
Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments. Related Articles Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments. J Bioinform Comput Biol. 2015 Jun 24;:1550020 Authors: Akhmedov M, «atay B, Apayd?n MS Abstract Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to...
nmrlearner Journal club 0 08-12-2015 10:04 PM
[NMR images] ... PROTEIN solubility determined with the OptiSol protein solubility
http://1.bp.blogspot.com/-7csMp0V8hEo/UXsrKtXoTPI/AAAAAAAAAGU/RIaxBdCKiTA/s640/increasing_solubility_fiv_matrix_protein_NMR_optisol.JPG 31/05/2014 1:57:49 PM GMT ... PROTEIN solubility determined with the OptiSol protein solubility More...
nmrlearner NMR pictures 0 05-31-2014 01:57 PM
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...
nmrlearner Journal club 0 02-11-2012 10:31 AM
Structures Behind the Amyloid Aggregation of ?-Synuclein: An NMR Based Approach.
Structures Behind the Amyloid Aggregation of ?-Synuclein: An NMR Based Approach. Structures Behind the Amyloid Aggregation of ?-Synuclein: An NMR Based Approach. Curr Protein Pept Sci. 2011 Feb 24; Authors: Orcellet ML, FernŠndez CO The misfolding of proteins into a toxic conformation is proposed to be at the molecular foundation of a number of neurodegenerative disorders including Alzheimer's and Parkinson's diseases. Evidence that ?-synuclein amyloidogenesis plays a causative role in the development of Parkinson's disease is furnished by a...
nmrlearner Journal club 0 02-26-2011 11:56 AM
Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies
Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies Abstract Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed...
nmrlearner Journal club 0 01-09-2011 12:46 PM
[NMR paper] Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures? Related Articles Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures? Proteins. 2005 Jul 1;60(1):139-47 Authors: Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures...
nmrlearner Journal club 0 12-01-2010 06:56 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 - 2017, 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 05:12 AM.


Map