NmrPipe

From NMR Wiki

author: Frank Delaglio
project page [1]
reference manual: [2]
newsgroup:nmrpipe@yahoo

NMRPipe is an extensive UNIX-based software system for processing, analyzing, and exploiting NMR spectroscopic data.

By the year 2009, NMRPipe has been used to help generate one-third of all NMR protein structures which have ever been measured, including roughly 70% of the NMR structures deposited in the PDB database in the last year.

The NMRPipe system consists of a collection of programs and scripts, along with a customized version of the TCL/TK interpreter which has been augmented with over 300 commands for manipulating spectral data and graphics, and molecular structures.

1 Spectral Processing, Display, and Analysis Features
2 Relating NMR parameters to molecular structure
3 Systems that run NMRPipe software
4 Manuals
5 References
6 Links

Spectral Processing, Display, and Analysis Features

Extraction of parameters for conversion of Bruker, Varian, and JEOL Delta format data, with conversion of time-domain data and adjustment for digitial oversampling. General-purpose format conversion tools are also provided.
Process, rephase and display multidimensional data, including options for Maximum Entropy (MEM) and Linear Prediction (LP) and Maximum Likelihood.
NMRPipe's pipeline-based processing schemes are intrinsically parallel, and multidimensional processing scripts can be easily modified for distributed processing in multi-CPU environments.
NMRPipe includes flexible methods to effectively replace bad values in multidimensional data using Linear Prediction.
NMRPipe provides a variety of approaches for reconstruction of Non-Uniform Sampled Data (NUS), using MEM, Maximum Likelihood, and Matrix Decomposition.
Automated Peak Detection for 1D-4D, with Interactive Editing and Annotation.
Extensive Line-Shape fitting functions, including direct fitting of pseudo-3D data such as relaxation series or J-modulated series.
Create simulated time or frequency domain data, including options for qualitative simulation of common spectra types such as HNCA.
Create and draw strip plots, projections, and overlays. Latest options include strip plots for multiple spectra, with drag and drop options to adjust strip order.

Relating NMR parameters to molecular structure

These features include a molecular dynamics engine for structure calculation, and unique structure calculation protocols based NMR homology of protein fragments:

Predict protein backbone angles based on backbone chemical shifts.
Simulate and display protein backbone chemical shifts based on backbone angles.
Calculate J-couplings from Karplus parameters.
Simulate or fit and display Dipolar Couplings.
Estimate protein alignment tensor parameters from measured dipolar couplings without prior knowledge of the structure.
Visualize tensor parameters with respect to a PDB file.
List or display Protein PDB backbone and sidechain angles, vizualize ramachandran trajectory for one or more proteins or fragments.
Analyze Protein PDB for H-bonds and secondary structure and turn classification.
Find coordinate or torsion RMSD between two or more structures, form overlay.
List, manipulate, and display structure parameters such as backbone angles.
Simulated annealing structure calculation, including NOEs, J-coupling, torsion restraints, radius of gyration, pseudo-contact shifts, and dipolar couplings.
Search the PDB Database for NMR Parameter Homology, using chemical shifts, dipolar couplings, etc.