NMRPipe

Reference: F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR. 6, 277-293 (1995).

NMRPipe provides comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. It is currently used in over 300 academic and commercial laboratories.

• Complete multidimensional processing schemes can be constructed as simple shell scripts, without the need to anticipate or explicitly specify data sizes. The dimensions can be processed and re-processed in any order, with the correct combination of real and imaginary data supplied automatically.
• Spectral axis calibrations are maintained during all stages of processing, so that processing parameters can be specified in terms of spectral units where desired.
• Comprehensive implementation of complex linear prediction (LP) and multi-dimensional maximum entropy method (nD-MEM) for reconstruction of truncated data, as well as complete and convenient inverse processing protocols required for their use.
• Convolution-based and polynomial solvent subtraction are provided, as well as automated and manual baseline corrections.
• Macro interpreter provides facilities for user-written processing functions in a subset of C.
• The pipeline approach is intrinsically parallel and automatically takes advantage of multi-cpu configurations. In addition, explicitly parallel schemes can also be constructed for balanced partitioning of processing tasks.
• Processed data can be used with well-known spectral analysis programs such as:



• ANSIG (Per Kraulis, Pharmacia)
• NMRView (Bruce Johnson, One Moon Scientific)
• PIPP (Dan Garrett, NIH)
• Sparky (Tom Goddard, UCSF)
• XEASY (Christian Bartels et al.)

• Conversion facilities specifically for Varian and Bruker binary time-domain data are provided, as well as general purpose facilities accommodating most other formats. All data is converted to a common format with a uniform organization of real and imaginary points.


• The conversion commands can read or write data from a command pipeline rather than a file, allowing such capabilities as conversion of compressed data, conversion of input data dispersed over more than one file, and processing schemes which go directly from spectrometer format to processed result.


• Dedicated interactive Varian conversion interface reads the procpar file and automatically extracts many acquisition parameters.


• Dedicated interactive Bruker conversion interface reads and interprets pulseprogram and acq files to deduce many acquisition parameters. Full compensation for Bruker digital filter format is performed during conversion.


• All conversion facilities support special options for complex acquisition schemes, including gradient-enhanced data (Rance-Kay/echo:anti-echo) and accommodation for interleaved data formats.

• Facilities to display and adjust NMRPipe-format file header information.
• Multi-dimensional lineshape fitting utility, including time-domain, frequency-domain, and hybrid models, and treatment of pseudo-3D data (e.g. relaxation series or coupling evolution data).
• Generation of peak evolutions from volume summation or Fourier-interpolated intensity.
• Facilities to simulate multidimensional time-domain and frequency-domain data from peak tables.
• Algebraic combination of spectra and FIDs.
• General purpose least-squares fitting utility with user-defined functions and Monte Carlo error analysis.
• Summary statistics of data from spectra or text tables.
• Principal Component Analysis (PCA)

NMRDraw

NMRWish

In addition to the usual features of Tcl/Tk, the special facilities of NMRWish include the following:

• Extraction or projection of arbitrary spectral Regions of Interest (ROIs), with options for centering and alignment, as well as automatic unfolding and sign-adjustment.
• Automated peak detection in 1D-4D, including options for identifying peaks due to random noise and truncation artifacts.
• Multi-window spectral graphics, with complete support of the usual Tk graphics canvas facilities.
• Scripts provide fully customizable PostScript output, including 1D and 2D extracts and projections, overlays, images, and strip plots.
• A simple, general purpose database engine, capable of manipulating peak tables, assignments, and PDB format molecular coordinates.
• General facilities for reading, writing, and manipulating binary data, including type conversion, general purpose vector processing, and access to NMRPipe processing functions.

DYNAMO

Additional Information: https://spin.niddk.nih.gov/bax-apps/NMRPipe/dynamo

DYNAMO is a structure calculation and analysis system built as an extension of our TCL/TK interpreter NMRWish, so that analysis schemes and annealing protocols are TCL scripts, and therefore relatively short, easy, and flexible.

DYNAMO includes a conventional cartesian coordinate simulated annealing engine, which supports restraints including:

• NOE derived interproton distance restraints.
• NMR derived torsion angle restraints.
• 3J coupling constants.
• Relative and absolute coordinate restraints.
• Radius of gyration.
• Dipolar couplings.
• Pseudo-Contact shifts.

In addition to simulated annealing structure calculation, DYNAMO scripts can be used for applications such as:

• List Backbone or Sidechain Angles in a Given Structure
• Change Backbone or Sidechain Angles in a Given Structure


• NMR Structure Prediction Using Simulated Annealing: ubiquitin


• Compute RMS Between Two Structures
• Compute Average Structure


• Simulate Chemical Shifts Based on Secondary Structure
• Simulate Dipolar Couplings
• Measure Alignment Tensor Parameters via Known Secondary Structure Elements


• Homology Search Based on Chemical Shifts
• Homology Search Base on Dipolar Couplings


• Visualize NMR Parameters

MFR - Molecular Fragment Replacement

Reference: F. Delaglio, G. Kontaxis, and A. Bax, Protein structure determination using molecular fragment replacement and NMR dipolar couplings, J. Am. Chem. Soc. 122, 2142-2143 (2000).

The MFR method determines elements of protein structure by finding small fragments (5-15 residues) in the PDB database whose simulated dipolar couplings or backbone chemical shifts match those measured for the target protein. These small homologous fragments can then be used in various ways to reconstitute larger elements of protein structure.

TALOS+

Contact:
shenyang@niddk.nih.gov
bax@nih.gov

References:

TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Bax
J. Biomol. NMR, 44 213-223 (2009).

Protein backbone angle restraints from searching a database for chemical shift and sequence homology.
Gabriel Cornilescu, Frank Delaglio, and Ad Bax
J. Biomol. NMR, 13 289-302 (1999).

Special Note: The original version of TALOS has been replaced by an improved version called TALOS+. This improved version is operated in much the same way as the original versions. TALOS+ was developed by Dr. Shen Yang in the Ad Bax group, and is now installed as an optional part of NMRPipe.

TALOS+ is a hybrid system for empirical prediction of protein phi and psi backbone torsion angles using chemical shifts and sequence. TALOS+ is an enhanced version of the earlier TALOS system which improves upon the original TALOS database mining approach by including a neural network classification scheme. This improved method provides a larger number of useful backbone angle predictions, 88% of residues in a given protein on average.

The original TALOS approach is an extension of the well-known observation that many kinds of secondary chemical shifts (i.e. differences between chemical shifts and their corresponding random coil values) are highly correlated with aspects of protein secondary structure. The goal of TALOS+ is to use secondary shift and sequence information in order to make quantitative predictions for the protein backbone angles phi and psi, and to provide a measure of the uncertainties in these predictions.

ACME

Reference: Frank Delaglio, Zhengrong Wu and Ad Bax: Measurement of Homonuclear Proton Couplings from Regular 2D COSY Spectra J. Magn. Reson., 149, 276-281 (2001).

Additional Information: https://spin.niddk.nih.gov/bax-apps/NMRPipe/acme

ACME is an interactive interface for measuring coupling constants from cross peaks in regular 2D COSY spectra. ACME is built from tools in the NMRPipe System.

The main idea behind ACME is that active couplings can be extracted accurately from individual COSY multiplets if the amplitude of the multiplet is known and held fixed during a fitting procedure. If the spin systems in the sample are fully relaxed, the amplitude will be uniform for all cross peaks, and it can be measured readily from one or more diagonal peaks. So, in practice, use of ACME will involve the following steps:

1. Measure COSY spectrum with conditions that allow the spin systems to be fully relaxed at the start of the COSY sequence.
2. A numerical diagonal processing scheme is used to prepare two versions of the COSY spectrum:
   • One version will contain the diagonal signals only, phased in absorptive mode. This version of the spectrum will be used to measure the amplitude.
   • The other version will contain the cross peaks only, with the diagonal numerically subtracted. This version will be used to measure active couplings in the cross peaks.
3. The ACME program will first be used in diagonal mode to fit one or more peaks in the diagonal-only spectrum. Fitting more than one diagonal peak will help establish average amplitude as well as its uncertainty.
4. Using the amplitude value determined from the diagonal, the ACME program will be used to measured the couplings in the cross peak spectrum:
   • Select a region to analyze from the spectrum
   • Insert signals at the approximate center of each multiplet of interest.
   • Specify the desired numbers of passive couplings for each multiplet.
   • Perform the fitting procedure, and inspect the results.