SPARTA+ Protein Backbone Chemical Shifts Prediction Program with a neural network

Download and Installation

A stable version SPARTA+ software package can be downloaded below. When downloading software from this website, you are agreeing to our Terms of Use, including the terms that there is no right to privacy on this system, and that the software from this website is not to be redistributed without permission from the authors. The SPARTA+ package provides the hardware & OS versions of linux9, and mac (see here for a definition of those hardware & OS versions by the NMRPipe system).

The most common SPARTA+ installation procedure on an Unix environment (linux9 and mac) will involve:

Create a directory for the SPARTA+ installation [for example, type mkdir /disk1/SPARTA+ in an "xterm" terminal window].

Go to the install directory [cd /disk1/SPARTA+].

Download and store the SPARTA+ installation files (sparta+.tar.Z) into the install directory

Via a web browser: Right-click the download links below and select "Save Target As", "Save Link As" or "Download Linked File (As)" (depending on the browser type), and save the files into the selected install directory (Be sure to retain the exact file name shown below).

Or via the unix command "wget":
wget https://spin.niddk.nih.gov/bax-apps/software/SPARTA+/sparta+.tar.Z

uncompress the package sparta+.tar.Z:
tar -zxvf sparta+.tar.Z

Execute the install.com script:

In most cases, no arguments will be required.

It will be sufficient to make the install scripts executable (by typing "chmod +x install.com"), then run the install.com script.

An initialization script sparta+Init.com will be generated, which stores the required and optional environment variable for running the program; it is recommended to use a common way to apply the initialization, i.e., adding the following lines to the ~/.cshrc file:
if (-e $SPARTAP_Dir/sparta+Init.com) then source $SPARTAP_Dir/sparta+Init.com endif
If the software is installed successfully and environmental variables are set up correctly, typing "sparta+" at any directory will print the SPARTA+ help information to the screen.

Note that, for the NMRPipe users, a separated installation of SPARTA+ as above is not needed, SPARTA+ is already installed as part of the NMRPipe package.

SPARTA+ can also be used on Windows systems (XP/7/10), which will involve:

Download and uncompress the package file sparta+.tar.Z to a local directory, e,g., C:/SPARTA+/

Run the program at any path by using the full path of SPARTA+ binary file for Windows system SPARTA+.static.winxp

C:/SPARTA+/bin/SPARTA+.static.winxp -in ref.pdb -spartaDir C:/SPARTA+

Note that the option -spartaDir must be provided!

There is a Web-Server version of SPARTA+ which can be used directly without installing SPARTA+. Users can access this Web-Sever system, along with other facilities for manipulating chemical shifts, dipolar couplings, and molecular structures at the Bax Group NMR Server site:

SPARTA+ Installation Files

SPARTA+ Web Server

(Version 2.9 Rev 2017.143.12.12)
sparta+.tar.Z [size: 6.24MB]

A list of 580 proteins (BMRB and PDB codes) used to train SPARTA+ can be downloaded here.

What is SPARTA+?
Reliability of SPARTA+
Components of the SPARTA+ Package
How to Use SPARTA+
Preparing the PDB Coordinates

About SPARTA+

SPARTA+ employs a well-trained neural network algorithm to make rapid chemical shift prediction on the basis of known structure. The input parameters for the neural network training procedure are similar to those used by the previous program SPARTA, hence the naming of this new program. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13Cβ chemical shifts are available. The neural network is well trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid and accurate chemical shift prediction for backbone and 13Cβ atoms.

top

Reliability of SPARTA+
The reliability of SPARTA+ approach was tested by a three-fold training-and-validation procedure during the neural network training procedure, as well as by a second validation of eleven proteins which are not present in the training database, for which the RMS deviations between the SPARTA+ predicted and experimental shifts are 2.45, 1.07, 0.92, 1.13, 0.25 and 0.49 ppm for 15N, 13C', 13Cα, 13Cβ, 1Hα and 1HN, respectively.

Moreover, SPARTA+ performs equally well for proteins without any homologous proteins in the database.
top

Components of the SPARTA+ Package
The SPARTA+ program is implemented using C++. The compiled executable files ("$SPARTAP_DIR/bin/SPARTA+.linux" for Linux, "$SPARTAP_DIR/bin/SPARTA+.winxp" for Windows, "$SPARTAP_DIR/bin/SPARTA+.mac" for Mac) or the starting script ("$SPARTAP_DIR/sparta+" for Linux/Mac) can be invoked with command-line arguments. A complete list of options can be invoked and generated with a "-help" command-line argument.
Use of SPARTA+ requires definition of an environment variable "SPARTAP_DIR" or a command-line argument "-spartaDir" to specify the SPARTA installation directory; it will be established automatically if run SPARTA from the starting script ("$SPARTAP_DIR/sparta+" in Linux/Mac), which includes the following lines:
setenv SPARTAP_DIR /disk1/SPARTA+/ $SPARTAP_DIR/bin/SPARTA+ $argv[1-$#argv]

Note that the definition of $SPARTAP_DIR in the starting script MUST be modified by users according to their SPARTA installation directory and the default "$SPARTA_DIR" is the current directory if not specified.
Other files of the SPARTA+ package include:

$SPARTAP_DIR/bin/SPARTA+.*
The compiled SPARTA+ binary files for multiple platforms, such as Linux (SPARTA+.linux, SPARTA+.static.linux), MacOS (SPARTA+.mac), SGI (SPARTA+.sgi6x) and WindowsXP/7/10 (SPARTA+.winxp, SPARTA+.static.winxp).
[Those binary files with an '.static' in the file name are compiled with all required running library files]

$SPARTAP_DIR/tab/randcoil.tab, rcadj.tab
The tables of random coil chemical shifts and adjustments values used in the shifts prediction process.

$SPARTAP_DIR/tab/*level*.tab
The weighting factors and biases of the neural network used in the prediction process.

$SPARTAP_DIR/test/*
The sample input PDB files and their SPARTA+ prediction result files.

top

How to Use SPARTA+
Use of SPARTA+ to predict backbone chemical shifts for one protein

Create a directory for the prediction session; all subsequent commands will be executed from this directory.
Prepare an input PDB coordinate file (for example "protein.pdb"), according to the format given below. Note that the hydrogen atoms must be present in the PDB coordinate file, a prediction with 'non-protonated' PDB coordinate input will yield significantly degraded accuracy!
Run SPARTA+ to perform the chemical shifts calculation. Most commonly, this will simply require a command such as:
   sparta+ -in protein.pdb
SPARTA+ first generates a "struct.tab" file from PDB coordinates, which contains of the phi, psi, chi1 and chi2 angles, H-bonding information and other structural parameters. A prediction summary file "pred.tab" (defined by -sum or -out option) will be created. The chemical shift calculation (after loading the parameters) will typically take <1 second for a 100-residue protein on a Linux PC with a 2.4GHz CPU.

Use of SPARTA+ to predict backbone chemical shifts for multiple proteins

Create a directory for the prediction session; all subsequent commands will be executed from this directory.
Prepare input PDB coordinate files (for example "protein1.pdb", ..., "proteinN.pdb"), according to the format given below.
Run the following SPARTA+ command line
   sparta+ -in protein1.pdb protein2.pdb ... proteinN.pdb

to perform the chemical shifts calculation for each of the input proteins. As results, a structural parameter table and a final prediction table file will be generated with an output name of {$PROTEIN_NAME}_struct.tab and {$PROTEIN_NAME}_pred.tab, respectively, for each input structure with a name of {$PROTEIN_NAME}.

Use of SPARTA+ to identify possible chemical shift referencing offsets and chemical shift outliers

If the experimental chemical shifts of the query protein are available (with a name "ref.tab", for example, and with TALOS format), SPARTA+ prediction can be performed by a command such as:

   sparta+ -in protein.pdb -ref ref.tab

SPARTA compares the predicted chemical shifts and the experimental shifts before exiting, and a prediction summary file "csCalc.tab" will be generated to store both the prediction results and the comparison between the experimental and SPARTA+ predicted shifts. If the average prediction error for a given chemical shift type exceeds 3 times expected errors (the standard deviation of the prediction errors divide the square root of the number of shifts), a warning will be printed to the screen with a suggestion of a reference correction for this type of chemical shift. A chemical shift outlier can be (manually) identified if the predicted chemical shift (value listed in the column SHIFT of the summary file csCalc.tab) deviates its experimental shift (value in the column CS_OBS) by more than five (estimated) standard deviation (value in the column SIGMA).
top

Preparing the Input PDB Coordinates
The input PDB coordinates should be prepared carefully with a proper format and naming conventions.

SPARTA+ accepts standard PDB coordinates file, but ONLY the FIRST conformer/chain will be used if more than one exist.

Hydrogen atoms must be present in the PDB coordinate file, a prediction with 'non-protonated' PDB coordinate input will yield significantly degraded accuracy! For PDB coordinates without hydrogen atoms, the hydrogen atoms can be added (by using the programs such as DYNAMO, REDUCE, MOLMOL, or any other similar programs) in order to get the hydrogen bonding information and ring current shifts.

For HA atoms of Glycine, a name of "HA2" or "HA3" should be used.
top

* All documents in PDF format require the free Adobe Acrobat Reader application for viewing

[ Home ] [ NIH ] [ NIDDK ] [ Terms of Use ]
last updated: July 21 2020 / ys