Wiki Tree Layout

From NESG Wiki
Revision as of 22:06, 5 November 2009 by Jma (talk | contribs)
Jump to navigation Jump to search

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

  1. Competition report
  2. Oligomerization state
  3. Mass spectrum
  4. Disorder prediction
  5. Pfam entry
  6. HSQC and protein concentration

NMR Data Collection

  1. Routine operation
    1. NMR sample tubes
    2. NMR Sample Preparation
    3. Inserting NMR Sample
    4. Tuning and matching
    5. Deuterium Lock
    6. Gradient shimming
    7. Shimming with the CHCl3 lineshape sample
    8. Pulse width calibration
    9. Temperature calibration
    10. Chemical shift referencing
  2. Advanced operation
    1. Deuterium pulse width calibration and decoupling
  3. NMR data acquisition for protein structure determination
    1. Custom NMR experiment setup scripts for VNMRJ
    2. 1D 1H NMR spectra and 2D [15N, 1H]-HSQC
    3. Estimation of correlation time of overall tumbling
    4. Estimation of measurement time
    5. NMR experiments for spin system identification
    6. 2D and 3D NOESY
    7. Double and triple NMR experiments
      1. 3D CBCA(CO)NH and HNCACB
      2. 3D HNCA and HN(CO)CA
      3. 3D HAHB(CO)NH
      4. (4,3)D CABCA(CO)NH and HNCACB
      5. (4,3)D HABCAB(CO)NH
      6. (H)CCH
      7. (H)CCH-TOCSY
      8. H(C)CH
      9. H(C)CH-TOCSY
      10. (4,3)D HCCH
    8. Other NMR experiments
      1. 2D [13C, 1H]-HSQC for 5% 13C-labeled samples
      2. 2D [15N, 1H]-long-range-HSQC for determination of histidine protomer state
      3. MEXICO
      4. CLEANEX
      5. H-D exchange experiment
      6. 15N spin relaxation parameters
  4. Advanced problems for data collection
    1. Setting up non-uniformly sampled spectra
      1. Guide for Varian/BioPack
      2. Guide for Bruker according to Arrowsmith group
  5. Maintenance
    1. VARIAN
      1. Installing and updating BioPack
      2. Full Probefile calibration
      3. Rebooting the console
      4. Cryoprobe conditioning
    2. BRUKER

NMR Data Processing

  1. General Priciples and Concepts
    1. Fourier transformation
      1. Zero-filling
      2. Apodization
      3. Phasing
      4. Linear prediction
      5. G-matrix Fourier transformation (GFT)
    2. Alternatives to Fourier transformation
      1. Maximum entropy reconstruction
      2. MDD reconstruction
      3. ...
  2. Practical Aspects
    1. NMRPIPE
      1. General information
      2. Buffalo's Processing Protocol using NMRpipe
    2. PROSA
    3. TOPSPIN
    4. AGNUS/AUTOPROC
    5. UBNMR
    6. Spectral format conversion


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.


  1. Principles and concepts
    1. Stable isotope labeling schemes
    2. NMR experiments
      1. Through-bond
      2. Through space
    3. Spin systems
      1. Definitions
      2. Identification
      3. Linking spin systems
      4. Matching onto covalent structure
  2. Practical aspects
    1. Semi-automated protocols
      1. CARA
      2. CCPN ANALYSIS
      3. NMRVIEW
      4. Sparky
      5. XEASY
        1. Spin system identification
        2. Backbone resonance assignment
          1. GFT-based spectra
            1. HNCACAB/CABCA(CO)NH
          2. Conventional spectra
            1. HNCACB/CBCA(CO)NH
            2. HNCA/HN(CO)CA
            3. HNCO/HN(CA)CO
            4. NOESY/TOCSY
        3. Side chain resonance assignment
          1. Aliphatic
            1. GFT NMR spectra
              1. (4,3)D GFT HABCAB(CO)NHN
              2. (4,3)D GFT HCCH
            2. Conventional spectra
              1. HAHB(CO)NH
              2. HCCH
              3. HCCH-TOCSY
              4. simultaneous NOESY
              5. (H)CC-TOCSY-(CO)NH
              6. H(CC-TOCSY-CO)NH
          2. Aromatic
            1. GFT-based spectra
            2. Conventional spectra
          3. Other
            1. Trp e1 NH and d1 CH
            2. Met e CH3
            3. Asn d2 and Gln e2 NH2
          4. NOESY peak integration
    2. Automated protocols
      1. AUTOASSIGN
      2. CLOUDS/ABACUS
      3. PINE
    3. Validation of resonance assignment
    4. Depositing chemical shifts


Structure Calculation and Validation

  1. Principles and concepts
    1. Constraints
      1. Distance (NOE, H-bond, distance calibration, NOE averaging, stereospecific assignments, PRE)
      2. Dihedral angle (J-coupling, chemical shifts)
      3. Orientational constraints (RDC, PRE)
    2. Advanced approaches to derive structural information
      1. SAXS
    3. Computational methods
    4. Assignment of NOESY peaklists and structure calculation
    5. Structure validation and quality assessment
  2. Practical aspects
    1. Structure calculation
      1. CYANA
        1. Getting started (init.cya, sequence, chemical shifts, peaks, macros/scripts, homodimers, cis-PRO, HIS protomer)
        2. Dihedral angle constraints (link to FOUND, CASHIFT, link to TALOS tutorial, J-couplings, converting TALOS to CYANA)
        3. Distance constraints (link to FOUND, various methods for NOE -> distance conversion, sum/average, stereospecific assignments, distance modification)
        4. Orientational restraints (RDCs) (link to REDCAT/PALES,FINDTENSOR, .rdc file, adding ORI to PDB file)
        5. FOUND
        6. Automated NOESY peaklist assignment (NOEASSIGN)
        7. Manual structure calculation
        8. Homodimer structure calculation
        9. GLOMSA
      2. AUTOSTRUCTURE
        1. Getting started (control file, GUI, cis-PRO)
        2. Dihedral angle constraints (HYPER)
        3. Distance constraints
        4. Automated NOESY peaklist assignment (NOEASSIGN)
        5. CYANA run
        6. XPLOR run
        7. RPF/DP scores
        8. Structure calculation using AS-DP
      3. CNS
        1. Getting started
        2. Preparation of input files for CNS
        3. Refinement in explicit water bath
      4. XPLOR
      5. CS-ROSETTA
      6. CS-DP ROSETTA
      7. RDC-ROSETTA
      8. RDC-assisted dimer structure calculation
      9. Special topics
        1. Protein-Ligand Complexes
        2. Metal Ions
        3. Dimers
        4. PRE constraints
    2. "Consensus" approaches
      1. Overview of Consensus Runs
      2. Finding Consensus NOE Assignments
      3. Validation of Consensus Runs
    3. Validation and deposition
      1. PSVS
      2. RPF Analysis
      3. MolProbity Server
      4. PdbStat
      5. PDB and BMRB Deposition
      6. ADIT-NMR
      7. HarvestDB
      8. SPINS

-- 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

 

Retrieved from "https://nesgwiki.chem.buffalo.edu/index.php?title=Wiki_Tree_Layout&oldid=1054"