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**[[Conditioning procedure for cryogenic probes]]   
**[[Conditioning procedure for cryogenic probes]]   
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== NMR data processing  ==


== NMR Resonance Assignment  ==
== NMR Resonance Assignment  ==
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== Structure Calculation and Validation  ==
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[[Structure Calculation and Validation|Principles and concepts]]
 
{| cellspacing="1"
 
|- valign="top"
#[[Resonance Assignment/Principles and concepts|Principles and concepts]]
|  
#[[Resonance Assignment/Practical aspects|Practical aspects]]
*Structure calculation  
##Semi-automated protocols
**CYANA
###[[CARA]]
**AutoStructure  
####[[Spin System Identification with CARA|Spin System Identification in 2D 15N-HSQC and 3D HNNCO]]
**[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]]  
####[[Backbone Assignment with CARA|Backbone Resonance Assignment]]
**[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]]  
####[[HA and HB Assignment with CARA|Assignment of HA and HB Resonances with (4,3)D GFT HABCAB(CO)NHN]]
**[[Structure Calculation Using CS-RDC-ROSETTA|CS-RDC-ROSETTA]]  
####Side Chain Assignment
**[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]<br>  
#####[[Aliphatic Side Chain Assignment with CARA|Aliphatic side-chain assignment]]
**"Consensus" approaches
#####[[Aromatic Side Chain Assignment with CARA|Aromatic side-chain assignment]]
|
#####[[Amide Side Chain Assignment with CARA|Amide side-chain assignment]]
*Special topics  
###[[Sparky]]
**[[Protein-Ligand Complexes|Protein-Ligand complexes]]  
###[[XEASY]]
**[[Working With Metal Ions|Metal ions]]  
####[[XEASY Spin system identification|Spin system identification]]
**[[Working With Dimers|Dimers]]  
####Backbone resonance assignment'''<br>'''
**[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]]  
#####GFT-based spectra
**[[REDCAT|REDCAT]] and [[REDCRAFT|REDCRAFT]]  
######[[HNCACAB/CABCA(CO)NH]]
**[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]]
#####Conventional spectra
|
######[[HNCACB/CBCA(CO)NH]]
*Structure Refinement  
######HNCA/HN(CO)CA
**[[Structure Refinement Using CNS Energy Minimization With Explicit Water|CNS refinement]]  
######HNCO/HN(CA)CO
**[[Structure Refinement Using XPLOR-NIH|XPLOR-NIH refinement]]  
######NOESY/TOCSY
**[[Rosetta High Resolution Protein Structure Refinement Protocol|ROSETTA refinement]]  
####[[XEASY Side Chain Assignment|Side chain resonance assignment]]
|
#####Aliphatic
*Validation and deposition  
######GFT NMR spectra
**[[PdbStat|PdbStat]]  
#######[[HA and HB Assignment with GFT in XEASY|(4,3)D GFT HABCAB(CO)NHN]]
**[[PSVS|PSVS]]  
#######[[Side chain assignment with aliphatic (4,3)D HCCH-COSY in XEASY|(4,3)D GFT HCCH]]
**[[RPF Analysis|RPF analysis]]  
######Conventional spectra
**[[MolProbity Server|MolProbity server]]  
#######HAHB(CO)NH
**[[PDB and BMRB Deposition|PDB and BMRB deposition]]  
#######HCCH-COSY
**[[ADIT-NMR|ADIT-NMR]]  
#######HCCH-TOCSY
**[[HarvestDB|HarvestDB]]  
#######[[Side chain assignment with CN-NOESY in XEASY|Simultaneous NOESY]]
**[[SPINS|SPINS]]
#######(H)CC-TOCSY-(CO)NH
|}
#######H(CC-TOCSY-CO)NH
#####[[Aromatic side chain assignment with Aro-HCCH-COSY in XEASY|Aromatic]]
######GFT-based spectra
######Conventional spectra
#####Other
######Trp e1 NH and d1 CH
######[[Met methyl assignment with NOESY|Met e CH3 ]]
######[[Amide Side Chain assignment with NOESY|Asn d2 and Gln e2 NH2]]
#####NOESY peak integration
##Automated protocols
###[[AutoAssign|AutoAssign]]
###[[AutoAssign WebServer|AutoAssign server]]
###[[Abacus|ABACUS]]
###[[The PINE Server|PINE server]]
##Validation of resonance assignment
###[[AVS|Assignment validation suite (AVS)]]
###[[LACS|Linear analysis of chemical shift (LACS)]]
##[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]
 
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=== Structure Calculation and Validation  ===
 
#[[Structure Calculation and Validation|Principles and concepts]]  
#Practical aspects
##Structure calculation
###CYANA
####[[CYANA|Getting started]]
####[[FOUND|FOUND]]
####[[TALOS|TALOS]]
####[[GLOMSA|GLOMSA]]
####[[NOE Calibration Using CYANA|NOE calibration]]
####[[Manual Structure Calculation Using CYANA|Manual structure calculation]]
####[[Automated NOESY Assignment Using CYANA|Automated NOESY assignment and structure calculation]]
####[[Structure Calculation With RDC's Using CYANA|Structure calculation with residual dipolar couplings]] (link to REDCAT/PALES,FINDTENSOR, .rdc file, adding ORI to PDB file)
####[[Homodimer Structure Calculation Using CYANA|Homodimer structure calculations]][[Homodimer Structure Calculation Using CYANA|<br>]]
###AutoStructure  
####[[AutoStructure/RPF Theory|Theory]]
####[[AutoStructure|Getting started]]
####[[CYANA Structure Calculations Using AutoStructure|CYANA run]]
####[[XPLOR Structure Calculations Using AutoStructure|XPLOR run]]
####[[Analyzing AutoStructure Output Directories|Analyzing the output]]
####[[RPF Analysis|RPF/DP scores]]
####[[Structure Calculation Using AS-DP|Structure calculation using AS-DP]]
###"Consensus"&nbsp;Approaches
####[[Overview of Consensus Runs|Overview of Consensus runs]]
####[[Finding Consensus NOE Assignments|Finding Consensus NOE assignments]]
####[[Validation of Consensus Run|Validation of Consensus runs]]
###[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]]  
###[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]]  
###[[Structure Calculation Using CS-RDC-ROSETTA|CS-RDC-ROSETTA]]  
###[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]<br>  
###Special topics  
####[[Protein-Ligand Complexes|Protein-Ligand complexes]]  
####[[Working With Metal Ions|Metal ions]]  
####[[Working With Dimers|Dimers]]  
####[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]]  
####[[REDCAT|REDCAT]]&nbsp;and [[REDCRAFT|REDCRAFT]]  
####[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]]  
##Structure Refinement  
###[[Structure Refinement Using CNS Energy Minimization With Explicit Water|CNS refinement]]  
###[[Structure Refinement Using XPLOR-NIH|XPLOR-NIH refinement]]  
###[[Rosetta High Resolution Protein Structure Refinement Protocol|ROSETTA refinement]]  
##Validation and deposition  
###[[PdbStat|PdbStat]]  
###[[PSVS|PSVS]]  
###[[RPF Analysis|RPF analysis]]  
###[[MolProbity Server|MolProbity server]]  
###[[PDB and BMRB Deposition|PDB and BMRB deposition]]  
###[[ADIT-NMR|ADIT-NMR]]  
###[[HarvestDB|HarvestDB]]  
###[[SPINS|SPINS]]
 
|}  
 
<br> <br>
 
== Getting started  ==
 
*[http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
*[http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
*[https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Revision as of 21:45, 2 December 2009


Welcome to the NESG Wiki!

For a more linear view of the contents see Wiki Tree Layout

Protein sample production

NMR Data Acquisition

NMR data processing

NMR Resonance Assignment

Structure Calculation and Validation

Principles and concepts

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