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 03-19-2020, 06:10 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 Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo-EM Maps

Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo-EM Maps


Angewandte Chemie International Edition, Accepted Article.

More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Neural network folds proteins a million times faster than its competitors - Chemistry World
Neural network folds proteins a million times faster than its competitors Chemistry WorldDespite knowing next to nothing about chemistry or biology, a neural network can make a good stab at one of the toughest problems in biochemistry – predicting ... Neural network folds proteins a million times faster than its competitors - Chemistry World More...
nmrlearner Online News 0 05-09-2019 05:55 AM
De novo protein structure determination from near-atomic-resolution cryo-EM maps - Nature.com
De novo protein structure determination from near-atomic-resolution cryo-EM maps - Nature.com <img alt="" height="1" width="1"> De novo protein structure determination from near-atomic-resolution cryo-EM maps Nature.com Despite these developments, little progress has been made in de novo model building into near-atomic-resolution cryo-EM density maps. Structural interpretation of cryo-EM maps typically starts with fitting an atomic X-ray or NMR structure into the map5. Read here
nmrlearner Online News 0 02-24-2015 02:48 PM
[NMR paper] Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N.
Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N. Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N. Methods Mol Biol. 2015;1260:17-32 Authors: Shen Y, Bax A Abstract Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to...
nmrlearner Journal club 0 12-17-2014 09:43 PM
[NMR paper] Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information. J Biomol NMR. 2013 Apr 28; Authors: Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M Abstract We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic...
nmrlearner Journal club 0 04-30-2013 10:21 PM
[NMR paper] Probability-based protein secondary structure identification using combined NMR chemi
Probability-based protein secondary structure identification using combined NMR chemical-shift data. Related Articles Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci. 2002 Apr;11(4):852-61 Authors: Wang Y, Jardetzky O For a long time, NMR chemical shifts have been used to identify protein secondary structures. Currently, this is accomplished through comparing the observed (1)H(alpha), (13)C(alpha), (13)C(beta), or (13)C' chemical shifts with the random coil values. Here, we...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins
RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins. Related Articles RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins. J Biomol NMR. 1999 Sep;15(1):15-26 Authors: Pons JL, Delsuc MA The assignment of the 1H spectrum of a protein or a polypeptide is the prerequisite for advanced NMR studies. We present here an assignment tool based on the artificial neural network technology, which determines the type of the amino acid from the chemical shift values observed in the 1H...
nmrlearner Journal club 0 11-18-2010 08:31 PM
NMR assignments and the identification of the secondary structure of the anti-retrovi
NMR assignments and the identification of the secondary structure of the anti-retroviral cytidine deaminase. Related Articles NMR assignments and the identification of the secondary structure of the anti-retroviral cytidine deaminase. Nucleic Acids Symp Ser (Oxf). 2008;(52):183-4 Authors: Furukawa A, Nagata T, Habu Y, Sugiyama R, Hayashi F, Yokoyama S, Takaku H, Katahira M APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G) is known to have a role in intrinsic cellular immunity against human immunodeficiency virus type1...
nmrlearner Journal club 0 11-17-2010 05:49 PM
[NMR paper] Using neural network predicted secondary structure information in automatic protein N
Using neural network predicted secondary structure information in automatic protein NMR assignment. Related Articles Using neural network predicted secondary structure information in automatic protein NMR assignment. J Chem Inf Comput Sci. 1997 Nov-Dec;37(6):1086-94 Authors: Choy WY, Sanctuary BC, Zhu G In CAPRI, an automated NMR assignment software package that was developed in our laboratory, both chemical shift values and coupling topologies of spin patterns are used in a procedure for amino acids recognition. By using a knowledge base of...
nmrlearner Journal club 0 08-22-2010 05:08 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 - 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 05:23 PM.


Map