NMR Spectroscopists' Corner

Services

Visualization server will generate DEVise visualizations for uploaded NMR-STAR 3.1 data tables.

STAR Data Table Generators

• NMR-STAR 3.1 Table Generator

• Protein Chemical Shift Table Generator
• Protein Coupling Constant Table Generator (requires Java 5)
• Protein Heteronuclear Relaxation Data Table Generator (requires Java 5)
• Protein H-exchange Rate Table Generator (requires Java 5)
   
• Nucleic Acid Chemical Shift Table Generator

NMR data file format conversion tools maintained by BMRB

• New STARch file converter -- converts data files in various formats to NMR-STAR 3.1 for upload to ADIT-NMR.
  Input formats include NMRView, PIPP, Sparky, XEASY, as well as tab- and comma-delimited.
• New RTF-gen: a tool to convert NMR-STAR 3.1 chemical shift tables into a publication format with Greek characters. RTF (Rich Text Format) can be imported into many word processors: Word, WordPerfect, and others.
• Old version of STARch converter: chemical shifts only.
• Old version of RTF-gen for NMR-STAR 2.1

NMR data file format conversion tools donated by the NMR community

• Publication format chemical shift tables to NMR-STAR format Tools to interconvert chemical shift data between a publication format and the NMR-STAR format. Also included are tools to calculate random coil chemical shifts and NMR experimental pulse lengths for experiments dependent on 3JHN(CA)HA coupling constants.
• FELIX to NMR-STAR Software to convert FELIX chemical shift files to NMR-STAR format.
• PIPP to NMR-STAR Software to convert PIPP chemical shift files to NMR-STAR format.
• NMR-STAR to TALOS Software to convert chemical shift tables in BMRB entries to TALOS input files.

Nomenclature and Defined Standards

Standardized Representation of NMR Data

• Amino Acid Atom nomenclature conversion table
• Amino Acid Pseudoatom nomenclature conversion table
   
• Nucleic Acid Pseudoatom nomenclature conversion table
   
• IUPAC Recomendations for the Presentation of NMR Structures of Proteins and Nucleic Acids
   
• Ligand Structures and Atom Nomenclature An ordered list of PDB heterogens and their PDB codes

Chemical Shift Reference Info

• Indirect Chemical Shift Referencing Ratios
• NMR Chemical Shift Referencing Molecules

Macromolecular Residue References

• Amino Acid Browser - Atom nomenclature, structure, properties, abbreviations, and for the 20 common L- Amino Acids
• Amino Acid Table References - Helix/sheet propensities, pKa values, codons, abbreviations, hydrophobicity, and molecular weights in table formats.
• Amino Acid Information from EMBL - NMR related amino acid information from the European Molecular Biology Laboratory
• Protein Calculator - Estimates pI, charge, UV absorbance, etc. From the Scripps Research Institute
   
• Atom nomenclature - Proton nomenclature for amino acids and Nucleic acids

Experimentally Determined Standards

Standard Shift Data for Amino Acids

• Standard Amino Acid 1H, 13C, and 15N Chemical Shifts
  Dyson, Wright, and coworkers
• Standard Amino Acid 1H and 13C Chemical Shifts
  Wuthrich and Coworkers
• Chemical Shift Index Parameters for Amino Acids (tar file)
  Dyson, Wright, and coworkers
  (brief documentation - tar file)
• Chemical Shift Index Parameters for Amino Acids
  Wishart and Coworkers

Other Structural Information

• Sequential and medium-range proton distances in polypeptide secondary structures - data table
• Secondary structure backbone proton-proton NOE intensities and secondary structure H-alpha to NH coupling constants

Software

NMR Software Maintained at BMRB

• AQUA Validation Server
• Wattos
  A software package consisting of programs for analyzing, annotating, parsing, archiving, and disseminating experimental NMR data deposited by authors world wide into the PDB

NMR Software Hosted at BMRB but Maintained by Other Users

• BBReader is a program to speed the search for information in NMR-STAR files.
• calc_cs - The program calculates random coil chemical shifts for a protein sequence
• calc - A program to calculate pulse lengths for NMR experiments.

Libraries

• Library of NMR Software
  Listing of the macros available
• Academic and Commercial Software is a collection of analytical tools hosted by members of the NMR community.

NMR Experiments and Pulse Programs

• Ad Bax Group
  Pulse Sequence Library
• BMRB Library of NMR Pulse Sequences
  Listing of the pulse sequences available
• GFT NMR Package G-matrix Fourier Transform Package
• Lewis Kay Lab Pulse Sequence Request Form
• NMR Pulse Programs from BMRB Time Domain Data Sets
• Art Palmer Group Bruker AMX Pulse Programs
• Pulse Sequence Library hosted by NMRFAM
• Michael Sattler Triple resonance pulse programs for 13C, 15N labeled proteins
• Solid State Pulse Programs from ENS Lyon
• Michael Summers Group NMR Toolkit at the Howard Hughes Medical Institute
• NMR Pulse Sequence Library of Carlsberg Laboratory
• CABM NMR Pulse Sequence Library at the Center for Advanced Biotechnology and Medicine - Rutgers
• Eric Zuiderweg Group University of Michigan - see bottom of page

Source References