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| **[[Conditioning procedure for cryogenic probes]] | | **[[Conditioning procedure for cryogenic probes]] |
| |} | | |} |
| | |
| | == NMR data processing == |
|
| |
|
| == NMR Resonance Assignment == | | == NMR Resonance Assignment == |
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| |} | | |} |
|
| |
|
| {|
| | == Structure Calculation and Validation == |
| | valign="top" style="border: 1px solid rgb(170, 170, 170); padding: 1em; background: rgb(232, 241, 255) none repeat scroll 0% 0%; width: 33%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;" |
| | [[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]]
| |
| | |
| | style="border: 1px solid rgb(170, 170, 170); padding: 1em; background: rgb(255, 239, 240) none repeat scroll 0% 0%; width: 33%; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;" |
| |
| === 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" 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]] 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]
| |