BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Software > NMR software
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 02-23-2012, 10:21 PM
markber's Avatar
Administrator
 
Join Date: Oct 2008
Posts: 1,538
Points: 35,627, Level: 100
Points: 35,627, Level: 100 Points: 35,627, Level: 100 Points: 35,627, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
Last Achievements
NMR Credits: 1,550
NMR Points: 35,627
Downloads: 17
Uploads: 4
Default GeNMR - template-based structure generation from NMR data

GeNMR website

GeNMR (GEnerate NMR structures) is a web server for template-based or ab initio generation of 3D protein structures using NOE-derived distance restraints and NMR chemical shifts. The web server produces an ensemble of PDB coordinates within a period ranging from 20 minutes to 4 hours, depending on protein size, server load, quality and type of experimental information, and selected protocol options.

References:

1. Berjanskii M, Tang P, Liang J, Cruz JA, Zhou J, Zhou Y, Bassett E, MacDonell C, Lu P, Lin G, Wishart DS. (2009)GeNMR: a web server for rapid NMR-based protein structure determination. 2009 Jul;37(Web Server issue):W670-7
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Descriptive Review of Current NMR-Based Metabolomic Data Analysis Packages
Descriptive Review of Current NMR-Based Metabolomic Data Analysis Packages Publication year: 2011 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 21 February 2011</br> Jose L., Izquierdo-García , Palmira, Villa , Angelos, Kyriazis , Laura del, Puerto-Nevado , Sandra, Pérez-Rial , ...</br> More...
nmrlearner Journal club 0 02-22-2011 11:00 AM
Error tolerant NMR backbone resonance assignment and automated structure generation.
Error tolerant NMR backbone resonance assignment and automated structure generation. Error tolerant NMR backbone resonance assignment and automated structure generation. J Bioinform Comput Biol. 2011 Feb;9(1):15-41 Authors: Alipanahi B, Gao X, Karakoc E, Li SC, Balbach F, Feng G, Donaldson L, Li M Error tolerant backbone resonance assignment is the cornerstone of the NMR structure determination process. Although a variety of assignment approaches have been developed, none works sufficiently well on noisy fully automatically picked peaks to enable...
nmrlearner Journal club 0 02-18-2011 08:07 PM
Incorporation of a Bioactive Reverse-Turn Heterocycle into a Peptide Template Using Solid-Phase Synthesis To Probe Melanocortin Receptor Selectivity and Ligand Conformations by 2D (1)H NMR.
Incorporation of a Bioactive Reverse-Turn Heterocycle into a Peptide Template Using Solid-Phase Synthesis To Probe Melanocortin Receptor Selectivity and Ligand Conformations by 2D (1)H NMR. Incorporation of a Bioactive Reverse-Turn Heterocycle into a Peptide Template Using Solid-Phase Synthesis To Probe Melanocortin Receptor Selectivity and Ligand Conformations by 2D (1)H NMR. J Med Chem. 2011 Feb 9; Authors: Singh A, Wilczynski A, Holder JR, Witek RM, Dirain ML, Xiang Z, Edison AS, Haskell-Luevano C By use of a solid-phase synthetic approach, a...
nmrlearner Journal club 0 02-11-2011 06:43 PM
[NMR paper] Druggability indices for protein targets derived from NMR-based screening data.
Druggability indices for protein targets derived from NMR-based screening data. Related Articles Druggability indices for protein targets derived from NMR-based screening data. J Med Chem. 2005 Apr 7;48(7):2518-25 Authors: Hajduk PJ, Huth JR, Fesik SW An analysis of heteronuclear-NMR-based screening data is used to derive relationships between the ability of small molecules to bind to a protein and various parameters that describe the protein binding site. It is found that a simple model including terms for polar and apolar surface area,...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Generation of native-like protein structures from limited NMR data, modern force fiel
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. Related Articles Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J Biomol NMR. 2005 Jan;31(1):59-64 Authors: Chen J, Won HS, Im W, Dyson HJ, Brooks CL Determining an accurate initial native-like protein fold is one of the most important and time-consuming steps of de novo NMR structure determination. Here we demonstrate that high-quality...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] The SHAPES strategy: an NMR-based approach for lead generation in drug discovery.
The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. Related Articles The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. Chem Biol. 1999 Oct;6(10):755-69 Authors: Fejzo J, Lepre CA, Peng JW, Bemis GW, Ajay , Murcko MA, Moore JM BACKGROUND: Recently, it has been shown that nuclear magnetic resonance (NMR) may be used to identify ligands that bind to low molecular weight protein drug targets. Recognizing the utility of NMR as a very sensitive method for detecting binding, we have...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[Stan NMR blog] Wavelet-based filtering applied to the diagonal suppression of 2D NMR data sets
Wavelet-based filtering applied to the diagonal suppression of 2D NMR data sets A novel 2D-NMR data-evaluation algorithm by Carlos Cobas. More...
nmrlearner News from NMR blogs 0 08-21-2010 06:14 PM
CING Common Interface for NMR structure Generation
CING Common Interface for NMR structure Generation More...
nmrlearner NMR bookmarks 0 08-19-2010 02:34 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 10:17 PM.


Map