NESG Wiki mediawiki_nesg https://nesgwiki.chem.buffalo.edu/index.php/Main_Page MediaWiki 1.38.2 first-letter Media Special Talk User User talk NESG Wiki NESG Wiki talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk Buffalo Buffalo talk NESG NESG talk 0 977 4368 4361 2022-11-29T02:29:40Z Suryaven 162 /* nmr 2.0 */ 4368 wikitext text/x-wiki __NOTOC__ <big>'''Welcome to the NESG Wiki!'''</big><br> 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 == {| cellspacing="1" class="FCK__ShowTableBorders" |- valign="top" | *[[Target selection|NESG target selection]] <br> *[[DNA cloning protocols|DNA cloning protocols]]<br> *[[Protein purification|Protein expression and purification protocols]]&nbsp;<br> *Sample Optimization **[[Construct optimization]] **[[Buffer optimization]] **[[Cofactor optimization]] | *Protein Sample Analysis **[[SDS page gel]] **[[Protein concentration|Protein concentration measurements]] **[[Oligomerization Status|Assessment of Oligomerization State]] ***[[Gel filtration and light scattering|gel-filtration and light scattering]] ***[[NMR determined Rotational correlation time]] **[[MassSpectrometry|Mass spectrum]] **[[NMR screening]] |} == NMR Data Acquisition == {| class="FCK__ShowTableBorders" cellspacing="1" |- valign="top" | *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]] |} == NMR Data Processing == {| class="FCK__ShowTableBorders" cellspacing="1" |- valign="top" | 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 ¹⁵N and ¹³C-edited experiments]] *[[HSQCTROSY RDC Measurement|2D ]]^{[[HSQCTROSY RDC Measurement|15]]}[[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 Resonance Assignment == *[[Resonance Assignment/Principles and concepts|Principles and concepts]] {| class="FCK__ShowTableBorders" cellspacing="1" |- valign="top" | *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" |- valign="top" | *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]] |} 0kedm5w21q0ylr8ak4nad8vd8lpz496