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__NOTOC__
__NOTOC__  


<big>'''Welcome to the NESG Wiki!'''</big><br>  
<big>'''Welcome to the NESG Wiki!'''</big><br>  


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


== Protein sample production  ==
Please check out [[NESG NMR wiki workshop at the 2010 Keystone meeting|NESG NMR wiki workshop presentations at the 2010 Keystone meeting]]


{| cellspacing="1"
== Protein Sample Production  ==
 
{| cellspacing="1" class="FCK__ShowTableBorders"
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**[[Construct optimization]]  
**[[Construct optimization]]  
**[[Buffer optimization]]  
**[[Buffer optimization]]  
**[[Cofactor optimization]]  
**[[Cofactor optimization]]
|
 
*[[SDS page gel]]  
|  
*[[Protein concentration|Protein concentration measurements]]  
*Protein Sample Analysis
*[[Oligomerization Status|Assessment of Oligomerization Status]]  
**[[SDS page gel]]  
**[[Gel filtration and light scattering|gel-filtration and light scattering]]  
**[[Protein concentration|Protein concentration measurements]]  
**[[NMR determined Rotational correlation time]]  
**[[Oligomerization Status|Assessment of Oligomerization State]]  
*[[MassSpectrometry|Mass spectrum]]  
***[[Gel filtration and light scattering|gel-filtration and light scattering]]  
*NMR screening
***[[NMR determined Rotational correlation time]]  
**[[1D screening|<sup>1</sup>H 1D screening]]  
**[[MassSpectrometry|Mass spectrum]]  
**[[Nhsqc screen|Initial [<sup>15</sup>N,<sup>1</sup>H] HSQC]]<br>
**[[NMR screening]]
 
 
 
|}
|}


== NMR Data Acquisition  ==
== NMR Data Acquisition  ==


{| cellspacing="1"
{| class="FCK__ShowTableBorders" cellspacing="1"
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*Routine operation  
*Routine operation  
**[[NMR sample tubes]]
**[[NMR Sample Preparation]]  
**[[NMR Sample Preparation]]  
**[[Inserting NMR Sample]]  
**[[Inserting NMR Sample]]  
**Tuning and matching  
**[[Tuning and matching]]
**[[Deuterium Lock]]  
**[[Deuterium Lock]]  
**[[Shimming]]  
**[[Shimming]]  
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*Advanced operation  
*Advanced operation  
**[[Deuterium pulse width calibration and decoupling]]
**[[Deuterium pulse width calibration and decoupling]]
|
 
|  
*NMR data acquisition for protein structure determination  
*NMR data acquisition for protein structure determination  
**[[Common NMR experiment sets]]  
**[[Common NMR experiment sets]]  
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**[[Simultaneous 13C,15N-resolved NOESY]]  
**[[Simultaneous 13C,15N-resolved NOESY]]  
**[[2D (13C, 1H) HSQC for fractionally 13C-labeled samples|2D [13C, 1H]-HSQC for fractionally 13C-labeled samples]]  
**[[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]]
**[[Long-range 15N-1H correlation experiments for histidine rings]]  
*Non-uniform sampling (NUS)
*[[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 Varian|NUS - Varian]]  
**[[Setting up non-uniformly sampled spectra/NUS guide for Bruker according to Arrowsmith group in Toronto|NUS - Bruker]]  
**[[Setting up non-uniformly sampled spectra/NUS guide for Bruker according to Arrowsmith group in Toronto|NUS - Bruker]]
|
 
*Maintenance (VARIAN)
|  
*Maintenance (VARIAN)  
**[[Installing and updating BioPack]]  
**[[Installing and updating BioPack]]  
**[[Full probefile calibration]]  
**[[Full probefile calibration]]  
**[[Rebooting spectrometer console]]  
**[[Rebooting spectrometer console]]  
**[[Conditioning procedure for cryogenic probes]]   
**[[Conditioning procedure for cryogenic probes]]
 
|}
 
== NMR Data Processing ==
 
{| class="FCK__ShowTableBorders" cellspacing="1"
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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]]
 
|
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 data processing  ==


== NMR Resonance Assignment  ==
== NMR Resonance Assignment  ==
*[[Resonance Assignment/Principles and concepts|Principles and concepts]]  
 
{| cellspacing="1"
*[[Resonance Assignment/Principles and concepts|Principles and concepts]]
 
{| class="FCK__ShowTableBorders" cellspacing="1"
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*Semi-automated protocols  
*Semi-automated protocols  
**[[Resonance Assignment/CARA|CARA]]
**[[Resonance Assignment/CARA|CARA]]  
**[[Sparky]]  
**[[Sparky]]  
**[[Resonance Assignment/XEASY|XEASY]]
**[[Resonance Assignment/XEASY|XEASY]]
|
 
|  
*Automated resonance assignment  
*Automated resonance assignment  
**[[AutoAssign|AutoAssign]]  
**[[AutoAssign|AutoAssign]]  
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**[[Abacus|ABACUS]]  
**[[Abacus|ABACUS]]  
**[[The PINE Server|PINE server]]
**[[The PINE Server|PINE server]]
|
 
|  
*Validation and deposition  
*Validation and deposition  
**[[AVS|Assignment validation suite (AVS)]]  
**[[AVS|Assignment validation suite (AVS)]]  
**[[LACS|Linear analysis of chemical shift (LACS)]]  
**[[LACS|Linear analysis of chemical shift (LACS)]]  
**[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]
**[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]]
|}
|}


== Structure Calculation and Validation  ==
== Structure Calculation and Validation  ==
[[Structure Calculation and Validation|Principles and concepts]]
 
{| cellspacing="1"
[[Structure Calculation and Validation|Principles and concepts]]  
 
{| class="FCK__ShowTableBorders" cellspacing="1"
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|  
*Structure calculation  
*Structure calculation  
**CYANA
**[[CYANA Structure Determination Program|CYANA]]
**AutoStructure  
**[[AutoStructure Structure Determination Program|AutoStructure]]
**[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]]  
**[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]]  
**[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]]  
**[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]]  
**[[Structure Calculation Using CS-RDC-ROSETTA|CS-RDC-ROSETTA]]  
**[[Structure Calculation Using CS-RDC-ROSETTA|CS-RDC-ROSETTA]]  
**[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]<br>
**[[Consensus Approaches|"Consensus" approaches]]  
**"Consensus" approaches
**[[Refinement Strategies|Refinement Strategies]]
|
 
|  
*Special topics  
*Special topics  
**[[Protein-Ligand Complexes|Protein-Ligand complexes]]  
**[[Protein-Ligand Complexes|Protein-Ligand complexes]]  
**[[Working With Metal Ions|Metal ions]]  
**[[Working With Metal Ions|Metal ions]]  
**[[Working With Dimers|Dimers]]
**[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]]  
**[[Residual Dipolar Couplings in Structure Refinement|Residual Dipolar Couplings]]  
**[[REDCAT|REDCAT]] and [[REDCRAFT|REDCRAFT]]  
**[[REDCAT|REDCAT]] and [[REDCRAFT|REDCRAFT]]  
**[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]]
**[[Paramagnetic Constraints in Structure Determination|Paramagnetic constraints]]  
|
**[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]
 
|  
*Structure Refinement  
*Structure Refinement  
**[[Structure Refinement Using CNS Energy Minimization With Explicit Water|CNS refinement]]  
**[[Structure Refinement Using CNS Energy Minimization With Explicit Water|CNS refinement]]  
**[[Structure Refinement Using XPLOR-NIH|XPLOR-NIH refinement]]  
**[[Structure Refinement Using XPLOR-NIH|XPLOR-NIH refinement]]  
**[[Rosetta High Resolution Protein Structure Refinement Protocol|ROSETTA refinement]]  
**[[Rosetta High Resolution Protein Structure Refinement Protocol|ROSETTA refinement]]<br>
|
 
|  
*Validation and deposition  
*Validation and deposition  
**[[PdbStat|PdbStat]]  
**[[PdbStat|PdbStat]]  
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**[[RPF Analysis|RPF analysis]]  
**[[RPF Analysis|RPF analysis]]  
**[[MolProbity Server|MolProbity server]]  
**[[MolProbity Server|MolProbity server]]  
**[[RDCvis & KiNG|RDCvis]]
**[[PDB and BMRB Deposition|PDB and BMRB deposition]]  
**[[PDB and BMRB Deposition|PDB and BMRB deposition]]  
**[[ADIT-NMR|ADIT-NMR]]  
**[[ADIT-NMR|ADIT-NMR]]  
**[[HarvestDB|HarvestDB]]  
**[[HarvestDB|HarvestDB]]  
**[[SPINS|SPINS]]
**[[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"