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Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
<big>'''Welcome to the NESG Wiki!'''</big><br>


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The NESG Wiki is a medium for sharing experimental protocols as well as training an educational materials in the fields of structural biology, structural genomics and biomolecular NMR.
 
Please check out [[NESG NMR wiki workshop at the 2010 Keystone meeting|NESG NMR wiki workshop presentations at the 2010 Keystone meeting]]
 
== Protein Sample Production  ==
 
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=== Protein sample production ===
*[[Target selection|NESG target selection]] <br>  
#[[Target selection|NESG target selection]] <br>
*[[DNA cloning protocols|DNA cloning protocols]]<br>  
#[[DNA cloning protocols|DNA cloning protocols]]<br>  
*[[Protein purification|Protein expression and purification protocols]]&nbsp;<br>  
#[[Protein purification|Protein expression and purification protocols]]&nbsp;<br>  
*Sample Optimization  
#Sample Optimization  
**[[Construct optimization]]  
##[[Construct optimization]]  
**[[Buffer optimization]]  
##[[Buffer optimization]]  
**[[Cofactor optimization]]
##[[Cofactor optimization]]  
 
#Initial protein analysis
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##[[SDS page gel]]  
*Protein Sample Analysis
##[[Protein concentration|Protein concentration measurements]]  
**[[SDS page gel]]  
##[[Oligomerization Status|Assessment of Oligomerization Status]]  
**[[Protein concentration|Protein concentration measurements]]  
###[[Gel filtration and light scattering|gel-filtration and light scattering]]  
**[[Oligomerization Status|Assessment of Oligomerization State]]  
###[[NMR determined Rotational correlation time]]  
***[[Gel filtration and light scattering|gel-filtration and light scattering]]  
##[[MassSpectrometry|Mass spectrum]]  
***[[NMR determined Rotational correlation time]]  
##NMR screening
**[[MassSpectrometry|Mass spectrum]]  
###[[1D screening|<sup>1</sup>H 1D screening]]
**[[NMR screening]]
###[[Nhsqc screen|Initial [<sup>15</sup>N,<sup>1</sup>H] HSQC]]<br>
 
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=== Resonance Assignment  ===
 
#[[Resonance Assignment/Principles and concepts|Principles and concepts]]
#[[Resonance Assignment/Practical aspects|Practical aspects]]
##Semi-automated protocols
###[[CARA]]
####[[Spin System Identification with CARA|Spin System Identification in 2D 15N-HSQC and 3D HNNCO]]
####[[Backbone Assignment with CARA|Backbone Resonance Assignment]]
####[[HA and HB Assignment with CARA|Assignment of HA and HB Resonances with (4,3)D GFT HABCAB(CO)NHN]]
####Side Chain Assignment
#####[[Aliphatic Side Chain Assignment with CARA|Aliphatic side-chain assignment]]
#####[[Aromatic Side Chain Assignment with CARA|Aromatic side-chain assignment]]
#####[[Amide Side Chain Assignment with CARA|Amide side-chain assignment]]
###[[Sparky]]
###[[XEASY]]
####[[XEASY Spin system identification|Spin system identification]]
####Backbone resonance assignment'''<br>'''
#####GFT-based spectra
######[[HNCACAB/CABCA(CO)NH]]
#####Conventional spectra
######[[HNCACB/CBCA(CO)NH]]
######HNCA/HN(CO)CA
######HNCO/HN(CA)CO
######NOESY/TOCSY
####[[XEASY Side Chain Assignment|Side chain resonance assignment]]
#####Aliphatic
######GFT NMR spectra
#######[[HA and HB Assignment with GFT in XEASY|(4,3)D GFT HABCAB(CO)NHN]]
#######[[Side chain assignment with aliphatic (4,3)D HCCH-COSY in XEASY|(4,3)D GFT HCCH]]
######Conventional spectra
#######HAHB(CO)NH
#######HCCH-COSY
#######HCCH-TOCSY
#######[[Side chain assignment with CN-NOESY in XEASY|Simultaneous NOESY]]
#######(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 RDC-ROSETTA|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]]
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== NMR Data Acquisition  ==


[[Wiki Tree Layout]]
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*Routine operation
**[[NMR Sample Preparation]]
**[[Inserting NMR Sample]]
**[[Tuning and matching]]
**[[Deuterium Lock]]
**[[Shimming]]
**[[Pulse width calibration]]
**[[Temperature calibration]]
**[[Chemical shift referencing]]
*Advanced operation
**[[Deuterium pulse width calibration and decoupling]]


|
*NMR data acquisition for protein structure determination
**[[Common NMR experiment sets]]
**[[NMR experiment setup scripts for VNMRJ|Custom NMR experiment setup scripts for VNMRJ]]
**[[Estimation of rotational correlation time]]
**[[Estimation of measurement time]]
**[[Simultaneous 13C,15N-resolved NOESY]]
**[[2D (13C, 1H) HSQC for fractionally 13C-labeled samples|2D [13C, 1H]-HSQC for fractionally 13C-labeled samples]]
**[[Long-range 15N-1H correlation experiments for histidine rings]]
*[[Setting up non-uniformly sampled spectra|Non-uniform sampling (NUS) ]]
**[[Setting up non-uniformly sampled spectra/NUS guide for Varian|NUS - Varian]]
**[[Setting up non-uniformly sampled spectra/NUS guide for Bruker according to Arrowsmith group in Toronto|NUS - Bruker]]


|
*Maintenance (VARIAN)
**[[Installing and updating BioPack]]
**[[Full probefile calibration]]
**[[Rebooting spectrometer console]]
**[[Conditioning procedure for cryogenic probes]]


== Getting started  ==
|}


*[http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]  
== NMR Data Processing  ==
*[http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]  
 
*[https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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NMRPipe
 
*[[Brief description of philosophy, commands, and functions of NMRPipe|Brief description of philosophy, commands, and functions]]
*[[Routine 2D Experiment|2D experiments]]
*[[Routine Processing Procedure for 3D 15N and 13C-edited Experiments|3D <sup>15</sup>N and <sup>13</sup>C-edited experiments]]
*[[HSQCTROSY RDC Measurement|2D ]]<sup>[[HSQCTROSY RDC Measurement|15]]</sup>[[HSQCTROSY RDC Measurement|N HSQC-TROSY experiment for RDC measurement]]
*[[Jmodulation Experiment RDC|2D J-modulation experiment for RDC measurement]]
*[[Alignment Media Preparation|Alignment Media Preparation for RDC measurement]]
 
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Other
 
*[[Processing NMR spectra with PROSA|PROSA]]
*[[Bruker Data Processing|TOPSPIN]]
*[[AGNuS/AutoProc|AUTOPROC]]  
*[[Processing non-uniformly sampled spectra with Multidimensional Decomposition|Processing NUS spectra with MDD]]
*[[Spectra Format Conversion from NMRPipe Data|NMRPipe processed data conversion to Sparky, CARA, XEASY, and NMRViewJ]]
 
|}
 
== NMR Resonance Assignment  ==
 
*[[Resonance Assignment/Principles and concepts|Principles and concepts]]
 
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*Semi-automated protocols
**[[Resonance Assignment/CARA|CARA]]
**[[Sparky]]
**[[Resonance Assignment/XEASY|XEASY]]
 
|
*Automated resonance assignment
**[[AutoAssign|AutoAssign]]
**[[AutoAssign WebServer|AutoAssign server]]
**[[Abacus|ABACUS]]
**[[The PINE Server|PINE server]]
 
|
*Validation and deposition
**[[AVS|Assignment validation suite (AVS)]]
**[[LACS|Linear analysis of chemical shift (LACS)]]
**[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]
 
|}
 
== Structure Calculation and Validation  ==
 
[[Structure Calculation and Validation|Principles and concepts]]
 
{| class="FCK__ShowTableBorders" cellspacing="1"
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*Structure calculation
**[[CYANA Structure Determination Program|CYANA]]
**[[AutoStructure Structure Determination Program|AutoStructure]]
**[[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]]
**[[Consensus Approaches|"Consensus" approaches]]
**[[Refinement Strategies|Refinement Strategies]]
 
|
*Special topics
**[[Protein-Ligand Complexes|Protein-Ligand complexes]]
**[[Working With Metal Ions|Metal ions]]
**[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]]
**[[REDCAT|REDCAT]] and [[REDCRAFT|REDCRAFT]]
**[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]]
**[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]
 
|
*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]]<br>
 
|
*Validation and deposition
**[[PdbStat|PdbStat]]
**[[PSVS|PSVS]]
**[[RPF Analysis|RPF analysis]]
**[[MolProbity Server|MolProbity server]]
**[[RDCvis & KiNG|RDCvis]]
**[[PDB and BMRB Deposition|PDB and BMRB deposition]]  
**[[ADIT-NMR|ADIT-NMR]]
**[[HarvestDB|HarvestDB]]
**[[SPINS|SPINS]]
 
|}

Latest revision as of 02:29, 29 November 2022


Welcome to the NESG Wiki!

The NESG Wiki is a medium for sharing experimental protocols as well as training an educational materials in the fields of structural biology, structural genomics and biomolecular NMR.

Please check out NESG NMR wiki workshop presentations at the 2010 Keystone meeting

Protein Sample Production


NMR Data Acquisition

NMR Data Processing

NMRPipe

Other

NMR Resonance Assignment

Structure Calculation and Validation

Principles and concepts

Retrieved from "https://nesgwiki.chem.buffalo.edu/index.php?title=Main_Page&oldid=4368"