Wiki Tree Layout
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
Compile Information on Protein Target
- Competition report
- Oligomerization state
- Mass spectrum
- Disorder prediction
- Pfam entry
- HSQC and protein concentration
NMR Data Collection
- Routine operation
- NMR sample tubes
- NMR Sample Preparation
- Inserting NMR Sample
- Tuning and matching
- Deuterium Lock
- Gradient shimming
- Shimming with the CHCl3 lineshape sample
- Pulse width calibration
- Temperature calibration
- Chemical shift referencing
- Advanced operation
- NMR data acquisition for protein structure determination
- Custom NMR experiment setup scripts for VNMRJ
- 1D 1H NMR spectra and 2D [15N, 1H]-HSQC
- Estimation of correlation time of overall tumbling
- Estimation of measurement time
- NMR experiments for spin system identification
- 2D and 3D NOESY
- 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 5% 13C-labeled samples
- 2D [15N, 1H]-long-range-HSQC for determination of histidine protomer state
- MEXICO
- CLEANEX
- H-D exchange experiment
- 15N spin relaxation parameters
- Advanced problems for data collection
- Setting up non-uniformly sampled spectra
- Guide for Varian/BioPack
- Guide for Bruker according to Arrowsmith group
- Setting up non-uniformly sampled spectra
- Maintenance
- VARIAN
- Installing and updating BioPack
- Full Probefile calibration
- Rebooting the console
- Cryoprobe conditioning
- BRUKER
- VARIAN
NMR Data Processing
- General Priciples and Concepts
- Fourier transformation
- Zero-filling
- Apodization
- Phasing
- Linear prediction
- G-matrix Fourier transformation (GFT)
- Alternatives to Fourier transformation
- Maximum entropy reconstruction
- MDD reconstruction
- ...
- Fourier transformation
- Practical Aspects
- NMRPIPE
- General information
- Buffalo's Processing Protocol using NMRpipe
- PROSA
- TOPSPIN
- AGNUS/AUTOPROC
- UBNMR
- Spectral format conversion
- NMRPIPE
Resonance Assignment
This chapter would focus on individual data analysis and resonance assignment packages, as most people stick to a particular software for entire structure determination projects.
- Principles and concepts
- Stable isotope labeling schemes
- NMR experiments
- Through-bond
- Through space
- Spin systems
- Definitions
- Identification
- Linking spin systems
- Matching onto covalent structure
- Practical aspects
- Semi-automated protocols
- CARA
- CCPN ANALYSIS
- NMRVIEW
- Sparky
- XEASY
- Spin system identification
- Backbone resonance assignment
- GFT-based spectra
- HNCACAB/CABCA(CO)NH
- Conventional spectra
- HNCACB/CBCA(CO)NH
- HNCA/HN(CO)CA
- HNCO/HN(CA)CO
- NOESY/TOCSY
- GFT-based spectra
- Side chain resonance assignment
- Aliphatic
- GFT NMR spectra
- (4,3)D GFT HABCAB(CO)NHN
- (4,3)D GFT HCCH
- Conventional spectra
- HAHB(CO)NH
- HCCH
- HCCH-TOCSY
- simultaneous NOESY
- (H)CC-TOCSY-(CO)NH
- H(CC-TOCSY-CO)NH
- GFT NMR spectra
- Aromatic
- GFT-based spectra
- Conventional spectra
- Other
- Trp e1 NH and d1 CH
- Met e CH3
- Asn d2 and Gln e2 NH2
- NOESY peak integration
- Aliphatic
- Automated protocols
- AUTOASSIGN
- CLOUDS/ABACUS
- PINE
- Validation of resonance assignment
- Depositing chemical shifts
- Semi-automated protocols
Structure Calculation and Validation
- Principles and concepts
- Constraints
- Distance (NOE, H-bond, distance calibration, NOE averaging, stereospecific assignments, PRE)
- Dihedral angle (J-coupling, chemical shifts)
- Orientational constraints (RDC, PRE)
- Advanced approaches to derive structural information
- SAXS
- Computational methods
- Assignment of NOESY peaklists and structure calculation
- Structure validation and quality assessment
- Constraints
- Practical aspects
- Structure calculation
- CYANA
- Getting started (init.cya, sequence, chemical shifts, peaks, macros/scripts, homodimers, cis-PRO, HIS protomer)
- Dihedral angle constraints (link to FOUND, CASHIFT, link to TALOS tutorial, J-couplings, converting TALOS to CYANA)
- Distance constraints (link to FOUND, various methods for NOE -> distance conversion, sum/average, stereospecific assignments, distance modification)
- Orientational restraints (RDCs) (link to REDCAT/PALES,FINDTENSOR, .rdc file, adding ORI to PDB file)
- FOUND
- Automated NOESY peaklist assignment (NOEASSIGN)
- Manual structure calculation
- Homodimer structure calculation
- GLOMSA
- AUTOSTRUCTURE
- Getting started (control file, GUI, cis-PRO)
- Dihedral angle constraints (HYPER)
- Distance constraints
- Automated NOESY peaklist assignment (NOEASSIGN)
- CYANA run
- XPLOR run
- RPF/DP scores
- Structure calculation using AS-DP
- CNS
- Getting started
- Preparation of input files for CNS
- Refinement in explicit water bath
- XPLOR
- CS-ROSETTA
- CS-DP ROSETTA
- RDC-ROSETTA
- RDC-assisted dimer structure calculation
- Special topics
- Protein-Ligand Complexes
- Metal Ions
- Dimers
- PRE constraints
- CYANA
- "Consensus" approaches
- 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