Wiki Tree Layout: Difference between revisions
mNo edit summary |
No edit summary |
||
(145 intermediate revisions by 9 users not shown) | |||
Line 9: | Line 9: | ||
Please leave your comments/suggestion at the bottom of this page | Please leave your comments/suggestion at the bottom of this page | ||
<br> | <br> | ||
= HTP NMR structure determination = | = HTP NMR structure determination = | ||
== | == Protein Target Selection, Sample Preparation, and Initial Screening == | ||
# | #[[Target selection|NESG target selection]] <br> | ||
#Oligomerization | #[[DNA cloning protocols|DNA cloning protocols]]<br> | ||
#[[MassSpectrometry|Mass spectrum]] | #[[Protein purification|Protein expression and purification protocols]] <br> | ||
# | #Sample Optimization | ||
# | ##[[Construct optimization]] | ||
##[[Buffer optimization]] | |||
##[[Cofactor optimization]] | |||
#Initial protein analysis | |||
##[[SDS page gel]] | |||
##[[Protein concentration|Protein concentration measurements]] | |||
##[[Oligomerization Status|Assessment of Oligomerization Status]] | |||
###[[Gel filtration and light scattering|gel-filtration and light scattering]] | |||
###[[NMR determined Rotational correlation time]] | |||
##[[MassSpectrometry|Mass spectrum]] | |||
##[[NMR screening]] | |||
<br> | |||
== NMR Data Collection == | == NMR Data Collection == | ||
Line 30: | Line 40: | ||
##Tuning and matching | ##Tuning and matching | ||
##[[Deuterium Lock]] | ##[[Deuterium Lock]] | ||
## | ##[[Shimming]] | ||
##[[Pulse width calibration]] | ##[[Pulse width calibration]] | ||
##[[Temperature calibration]] | ##[[Temperature calibration]] | ||
##[[Chemical shift referencing]] | ##[[Chemical shift referencing]] | ||
#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 | ||
##Custom NMR experiment setup scripts for VNMRJ | ##[[Common NMR experiment sets]] | ||
##[[NMR experiment setup scripts for VNMRJ|Custom NMR experiment setup scripts for VNMRJ]] | |||
##1D 1H NMR spectra and 2D [15N, 1H]-HSQC | ##1D 1H NMR spectra and 2D [15N, 1H]-HSQC | ||
##Estimation of correlation time | ##[[Estimation of rotational correlation time]] | ||
##Estimation of measurement time | ##[[Estimation of measurement time]] | ||
##NMR experiments for spin system identification | ##NMR experiments for spin system identification | ||
##2D and 3D NOESY | ##2D and 3D NOESY experiments | ||
###[[Simultaneous 13C,15N-resolved NOESY]] | |||
##Double and triple NMR experiments | ##Double and triple NMR experiments | ||
###3D CBCA(CO)NH and HNCACB | ###3D CBCA(CO)NH and HNCACB | ||
Line 54: | Line 65: | ||
###H(C)CH | ###H(C)CH | ||
###H(C)CH-TOCSY | ###H(C)CH-TOCSY | ||
###(4,3)D HCCH | ###(4,3)D HCCH | ||
##Other NMR experiments | ##Other NMR experiments | ||
###2D [13C, 1H]-HSQC for | ###[[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]] - determination of histidine isoprotomer state | ||
###MEXICO | ###MEXICO | ||
###CLEANEX | ###CLEANEX | ||
###H-D exchange experiment | ###H-D exchange experiment | ||
###15N spin relaxation parameters | ###15N spin relaxation parameters | ||
#Advanced problems for data collection | #Advanced problems for data collection | ||
##Setting up non-uniformly sampled spectra | ##[[Setting up non-uniformly sampled spectra]] | ||
###Guide for Varian/BioPack | ###[[Setting up non-uniformly sampled spectra/NUS guide for Varian|Guide for Varian/BioPack]] | ||
###Guide for Bruker according to Arrowsmith group | ###[[Setting up non-uniformly sampled spectra/NUS guide for Bruker according to Arrowsmith group in Toronto|Guide for Bruker/Topspin according to Arrowsmith group]] | ||
#Maintenance | #Maintenance | ||
##VARIAN | ##VARIAN | ||
###Installing and updating | ###[[Installing and updating BioPack]] | ||
###Full | ###[[Full probefile calibration]] | ||
###Rebooting | ###[[Rebooting spectrometer console]] | ||
### | ###[[Conditioning procedure for cryogenic probes]] | ||
##BRUKER | ##BRUKER | ||
== NMR Data Processing == | == NMR Data Processing == | ||
# | #Processing Procedures for Routine Experiments<br> | ||
## | ##NMRPipe | ||
### | ###[[Brief description of philosophy, commands, and functions of NMRPipe|Brief description of philosophy, commands, and functions of NMRPipe]] | ||
### | ###[[Routine 2D Experiment|Routine Processing Procedure for 2D Experiment]]<sup></sup> | ||
### | ###[[Routine Processing Procedure for 3D 15N and 13C-edited Experiments|Routine Processing Procedure for 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]] | ||
## | ###[[Processing NMR spectra with UB PERL scripts|Routine processing of spectra using Buffalo-developed PERL scripts]] | ||
# | ##[[Processing NMR spectra with PROSA|PROSA]] | ||
## | ##[[Bruker Data Processing|TOPSPIN]] | ||
## | ##[[AGNuS/AutoProc|AUTOPROC]] | ||
##[[UBNMR|UBNMR]] | |||
## | #Processing Procedures for Alternative Data Collection Methods | ||
## | ##G-Matrix Fourier transformation (GFT) | ||
# | ##[[Processing non-uniformly sampled spectra with Multidimensional Decomposition|Processing non-uniformly sampled spectra with Multidimensional Decomposition]] | ||
## | #Spectra Format Conversion | ||
## | ##[[Spectra Format Conversion from NMRPipe Data|NMRPipe processed data conversion to Sparky, CARA, XEASY, and NMRViewJ]] | ||
# | ##TOPSPIN processed data conversion to Sparky, CARA, XEASY, and NMRViewJ<br> | ||
## | |||
## | |||
<br> | |||
== Resonance Assignment == | == Resonance Assignment == | ||
This chapter | This chapter focuses on data analysis and resonance assignment packages, as most people stick to a particular software for entire structure determination projects. | ||
<br> | <br> | ||
#Principles and concepts | #[[Resonance Assignment/Principles and concepts|Principles and concepts]] | ||
# | #[[Resonance Assignment/Practical aspects|Practical aspects]] | ||
##Semi-automated protocols | ##Semi-automated protocols | ||
###CARA | ###[[Resonance Assignment/CARA|CARA]] | ||
### | ####[[Spin System Identification with CARA|Spin System Identification in 2D 15N-HSQC and 3D HNNCO]] | ||
### | ####[[Backbone Assignment with CARA|Backbone Resonance Assignment]] | ||
###[[Sparky| | ####[[HA and HB Assignment with CARA|Assignment of HA and HB Resonances with (4,3)D GFT HABCAB(CO)NHN]] | ||
###XEASY | ####Side Chain Assignment | ||
####[[ | #####[[Aliphatic Side Chain Assignment with CARA|Aliphatic side-chain assignment]] | ||
####Backbone resonance assignment'''<br>''' | #####[[Aromatic Side Chain Assignment with CARA|Aromatic side-chain assignment]] | ||
#####[[Amide Side Chain Assignment with CARA|Amide side-chain assignment]] | |||
###[[Sparky]] | |||
###[[Resonance Assignment/XEASY|XEASY]] | |||
####[[XEASY Introduction|Introduction]] | |||
####[[XEASY Spin system identification|Spin system identification]] | |||
####Backbone resonance assignment'''<br>''' | |||
#####GFT-based spectra | #####GFT-based spectra | ||
######HNCACAB/CABCA(CO)NH | ######[[HNCACAB/CABCA(CO)NH]] | ||
#####Conventional spectra | #####Conventional spectra | ||
######HNCACB/CBCA(CO)NH | ######[[HNCACB/CBCA(CO)NH]]<br> | ||
####Side chain resonance assignment | ####Side chain resonance assignment | ||
#####Aliphatic | #####Aliphatic | ||
######GFT | ######GFT-based spectra | ||
#######(4,3)D GFT HABCAB(CO)NHN | #######[[HA and HB Assignment with GFT in XEASY|(4,3)D GFT HABCAB(CO)NHN]] | ||
#######(4,3)D GFT HCCH | #######[[Side chain assignment with aliphatic (4,3)D HCCH-COSY in XEASY|(4,3)D GFT HCCH]] | ||
######Conventional spectra | ######Conventional spectra | ||
#######HAHB(CO)NH | #######HAHB(CO)NH | ||
#######HCCH | #######HCCH-COSY<br> | ||
####### | #######[[Side chain assignment with CN-NOESY in XEASY|Simultaneous NOESY]] | ||
#####[[Aromatic side chain assignment with Aro-HCCH-COSY in XEASY|Aromatic]] | |||
##### | |||
#####Other | #####Other | ||
######Trp e1 NH and d1 CH | ######Trp e1 NH and d1 CH | ||
######Met e CH3 | ######[[Met methyl assignment with NOESY|Met e CH3 ]] | ||
######Asn d2 and Gln e2 NH2 | ######[[Amide Side Chain assignment with NOESY|Asn d2 and Gln e2 NH2]] | ||
####NOESY peak integration | |||
##Automated protocols | ##Automated protocols | ||
### | ###[[AutoAssign|AutoAssign]] | ||
### | ###[[AutoAssign WebServer|AutoAssign server]] | ||
###PINE | ###[[Abacus|ABACUS]] | ||
###[[The PINE Server|PINE server]] | |||
##Validation of resonance assignment | ##Validation of resonance assignment | ||
##Depositing chemical shifts | ###[[AVS|Assignment validation suite (AVS)]] | ||
###[[LACS|Linear analysis of chemical shift (LACS)]] | |||
##[[PDB and BMRB Deposition#Preparing_files_for_BMRB_depostion|Depositing chemical shifts]] | |||
<br> | <br> | ||
Line 162: | Line 161: | ||
== Structure Calculation and Validation == | == Structure Calculation and Validation == | ||
#Principles and concepts | #[[Structure Calculation and Validation|Principles and concepts]] | ||
#Practical aspects | #Practical aspects | ||
##Structure calculation | ##Structure calculation | ||
###CYANA | ###CYANA | ||
####Getting started | ####[[CYANA|Getting started]] | ||
####[[FOUND|FOUND]] | ####[[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|Getting started]] | ||
####CYANA run | ####[[CYANA Structure Calculations Using AutoStructure|CYANA run]] | ||
####XPLOR run | ####[[XPLOR Structure Calculations Using AutoStructure|XPLOR run]] | ||
####RPF/DP scores | ####[[Analyzing AutoStructure Output Directories|Analyzing the output]] | ||
####Structure calculation using AS-DP | ####[[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]] | ||
###CS-ROSETTA | ###[[Structure Calculation Using CS-Rosetta|CS-ROSETTA]] | ||
###[[Structure Calculation Using CS-DP ROSETTA|CS-DP ROSETTA]] | |||
###RDC-ROSETTA | ###[[Structure Calculation Using CS-RDC-ROSETTA|CS-RDC-ROSETTA]] | ||
###[[RDC- | ###[[RDC-Assisted Dimer Structure Determination|RDC-assisted dimer structure calculation]]<br> | ||
###Special topics | ###Special topics | ||
####[[ | ####[[Protein-Ligand Complexes|Protein-Ligand complexes]] | ||
####Metal Ions | ####[[Working With Metal Ions|Metal ions]] | ||
####Dimers | ####[[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 | ##Validation and deposition | ||
###[[PdbStat|PdbStat]] | |||
###[[PSVS|PSVS]] | ###[[PSVS|PSVS]] | ||
###[[ | ###[[RPF Analysis|RPF analysis]] | ||
###[[MolProbity | ###[[MolProbity Server|MolProbity server]] | ||
###[[ | ###[[PDB and BMRB Deposition|PDB and BMRB deposition]] | ||
###[[ADIT-NMR|ADIT-NMR]] | ###[[ADIT-NMR|ADIT-NMR]] | ||
###[[HarvestDB|HarvestDB]] | ###[[HarvestDB|HarvestDB]] |
Latest revision as of 20:51, 14 December 2009
This outline of the NESG NMR Wiki is designed to expand on the existing "Master Recipe" and should serve as an experience harvesting tool.
- It has a rather broad coverage to facilitate long-tewrm growth and development. Aditional compact aggregator pages may be needed to pesent specific information concisely.
- There would be separate webs within the wiki: Public(or Main), NESG, and member lab webs. Most common knowlege topics should be public, unless they are specific to NESG
- We assume that the target audience has some knowledge about NMR and protein structure determination, but make the content useful for training
- "Resonance Assignment" and "Structure Determination" chaptes would focus on individual software packages. The XEASY resonance assignment tree, as the most complete, would serve as a template for other software.
- Most chapters should include a "general principles" section.
Please leave your comments/suggestion at the bottom of this page
HTP NMR structure determination
Protein Target Selection, Sample Preparation, and Initial Screening
- NESG target selection
- DNA cloning protocols
- Protein expression and purification protocols
- Sample Optimization
- Initial protein analysis
NMR Data Collection
- Routine operation
- Advanced operation
- NMR data acquisition for protein structure determination
- Common NMR experiment sets
- Custom NMR experiment setup scripts for VNMRJ
- 1D 1H NMR spectra and 2D [15N, 1H]-HSQC
- Estimation of rotational correlation time
- Estimation of measurement time
- NMR experiments for spin system identification
- 2D and 3D NOESY experiments
- Double and triple NMR experiments
- 3D CBCA(CO)NH and HNCACB
- 3D HNCA and HN(CO)CA
- 3D HAHB(CO)NH
- (4,3)D CABCA(CO)NH and HNCACB
- (4,3)D HABCAB(CO)NH
- (H)CCH
- (H)CCH-TOCSY
- H(C)CH
- H(C)CH-TOCSY
- (4,3)D HCCH
- Other NMR experiments
- 2D [13C, 1H]-HSQC for fractionally 13C-labeled samples
- Long-range 15N-1H correlation experiments for histidine rings - determination of histidine isoprotomer state
- MEXICO
- CLEANEX
- H-D exchange experiment
- 15N spin relaxation parameters
- Advanced problems for data collection
- Maintenance
NMR Data Processing
- Processing Procedures for Routine Experiments
- NMRPipe
- Brief description of philosophy, commands, and functions of NMRPipe
- Routine Processing Procedure for 2D Experiment
- Routine Processing Procedure for 3D 15N and 13C-edited Experiments
- 2D 15N HSQC-TROSY experiment for RDC measurement
- 2D J-modulation experiment for RDC measurement
- Routine processing of spectra using Buffalo-developed PERL scripts
- PROSA
- TOPSPIN
- AUTOPROC
- UBNMR
- NMRPipe
- Processing Procedures for Alternative Data Collection Methods
- G-Matrix Fourier transformation (GFT)
- Processing non-uniformly sampled spectra with Multidimensional Decomposition
- Spectra Format Conversion
- NMRPipe processed data conversion to Sparky, CARA, XEASY, and NMRViewJ
- TOPSPIN processed data conversion to Sparky, CARA, XEASY, and NMRViewJ
Resonance Assignment
This chapter focuses on data analysis and resonance assignment packages, as most people stick to a particular software for entire structure determination projects.
- Principles and concepts
- Practical aspects
- Semi-automated protocols
- CARA
- Sparky
- XEASY
- Introduction
- Spin system identification
- Backbone resonance assignment
- GFT-based spectra
- Conventional spectra
- Side chain resonance assignment
- Aliphatic
- GFT-based spectra
- Conventional spectra
- HAHB(CO)NH
- HCCH-COSY
- Simultaneous NOESY
- Aromatic
- Other
- Trp e1 NH and d1 CH
- Met e CH3
- Asn d2 and Gln e2 NH2
- Aliphatic
- NOESY peak integration
- Automated protocols
- Validation of resonance assignment
- Depositing chemical shifts
- Semi-automated protocols
Structure Calculation and Validation
- Principles and concepts
- Practical aspects
- Structure calculation
- CYANA
- Getting started
- FOUND
- TALOS
- GLOMSA
- NOE calibration
- Manual structure calculation
- Automated NOESY assignment and structure calculation
- Structure calculation with residual dipolar couplings (link to REDCAT/PALES,FINDTENSOR, .rdc file, adding ORI to PDB file)
- Homodimer structure calculations
- AutoStructure
- "Consensus" Approaches
- CS-ROSETTA
- CS-DP ROSETTA
- CS-RDC-ROSETTA
- RDC-assisted dimer structure calculation
- Special topics
- CYANA
- Structure Refinement
- Validation and deposition
- Structure calculation
-- JeffMills - 28 May 2009
Here are two comments from Guy:
- need to have centralized site for downloading all software that NESG has developed or licensed; this would be a central site for NESG scientists to use to access the latest version of all software
- need to allow outside users to access links to all software (they will need licenses to download) and also to download software from NESG
-- AlexEletski - 13 Jul 2009