NMR Spectroscopists' Corner

STAR Data Table Generators

• Table Generator: creates template NMR-STAR 3.1 data tables from residue sequence string.

NMR data file format conversion tools maintained by BMRB

• 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.
• Ambiguity code assignment interface: simplifies assignment of chemical shift ambiguity codes.
• 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.
• NMR-STAR 3.1 table converter: converts NMR-STAR 3.1 data tables to NMR-STAR 2.1 or other formats.

• Old version of RTF-gen for NMR-STAR 2.1

NMR data file format conversion tools donated by the NMR community

• tab2bmrb: convert chemical shift tables between publication format and NMR-STAR 2.1 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 for converting FELIX chemical shift files to NMR-STAR 2.1 format.
• PIPP to NMR-STAR: software for converting PIPP chemical shift files to NMR-STAR 2.1 format.
• NMR-STAR to TALOS: software for converting chemical shift tables in BMRB entries to TALOS input files.
• CYANA to XPLOR: script for converting CYANA formatted files to XPLOR/CNS/PDB 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

Chemical Shift Reference Info

• Indirect Chemical Shift Referencing Ratios

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

• 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

Structure and Dynamics software using NMR data

• NMR-relax Protein dynamics by NMR relaxation data analysis.
• CS-Rosetta - System for chemical shifts based protein structure prediction using ROSETTA
• CS-Rosetta structure calculation
• SimShiftDB - Homology search algorithm based on chemical shifts - Center of Applied Molecular Engineering, the University of Salzburg, Austria. (Firefox is recommended for SimShiftDB.)
• POP cis/trans prediction based on 13C chemical shifts
• CNSsolve - Crystallography & NMR System (CNS) is designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination.
• Tensor - A program for treating solution state 15N relaxation for the study of molecular dynamics.
• Module - A program developed to allow the determination of alignment tensor parameters for individual or multiple domains in macromolecules from residual dipolar couplings and to facilitate their manipulation to construct low-resolution models of macromolecular structure.
• Wishart Research Group webservers
• SHIFTX Web Server - A web server that predicts 1H, 13C, and 15N protein chemical shifts using the 3D structure (PDB coordinates) of the protein of interest.
• THRIFTY Web Server - A web server that rapidly generates 3D protein structures (PDB coordinates) from their corresponding chemical shift assignments

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.

Miscellanious

• Eiso AB's script page various gawk scripts for handling NMR data

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
• NESG Wiki a medium for sharing experimental protocols as well as training and educational materials
• NMR Pulse Programs from BMRB Time Domain Data Sets
• Art Palmer Group Bruker AMX Pulse Programs
• Software and Pulse Sequences hosted by NMRFAM
• 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