TOPOLINK

A package to evaluate structural models using chemical crosslinking distance constraints.

Institute of Chemistry
University of Campinas

TopoLink:
Home
Server
Download
Usage
Tools
XLFF
XL Statistics
See also:
Dalton MS lab
SIM-XL
G-score
LovoAlign
Packmol
MDLovoFit
Group software page
The TANGO project
Home Server Download
TopoLink is FREE software. It can be used, copied and distributed according to the General Public License v3.0. In order to keep our motivation in developing and distributing the package, please cite:
A. J. R. Ferrari, M. A. Clasen, L. Kurt, P. C. Carvalho, F. C. Gozzo, L Martínez
TopoLink: Evaluation structural models using chemical crosslinking distance constraints.
Bioinformatics, 35(17), 3169-3170, 2019. [LINK]
Windows 10 (64 bits) version with graphical user interface:
Download the zip file, extract it and execute the TopolinkUI_Installer:

[GUI - Installer - ZIP file]

(for all features, PyMol must be installed)


The graphical user interface is developed by the PatternLab for Proteomics group: PatternLab


[Click to enlarge]
Standalone executable for Windows 10 (64 bits) (for command-line use)

Download the executable from here: [topolink.exe Win10-x86_64]

Save the executable and add the path to it in your PATH environment variable. The package is run from the command prompt as indicated in the user guide.

Multi-platform source code for command line use

Download the latest version of the package from this site. To compile it, first, you need a Fortran compiler. The GNU Fortran Compiler, gfortran, is available in standard repositories of every GNU-Linux distribution.

If you have a Fortran compiler installed, do:
tar -xzf topolink-{version}.tar.gz
cd topolink/src
make
This procedure will create the executable topolink in the directory topolink/bin. The most practical way to use it is to add this directory to your path.

Go to the Usage page for instructions on how to use the software.

GIT repository: https://gibhub.com/m3g/topolink

All version
FileDescription
topolink-19.156.tar.gz Released on Jun 05, 2019 - [change log at github]
topolink-19.066.tar.gz Released on Mar 07, 2019 - [change log at github]
topolink-19.032.tar.gz Released on Feb 01, 2019 - [change log at github]
topolink-19.020.tar.gz Released on Jan 20, 2019 - [change log at github]
topolink-18.336.tar.gz Released on Dec 02, 2018 - [change log at github]
topolink-18.335.tar.gz Released on Dec 01, 2018 - [change log at github]
topolink-18.324.tar.gz Released on Nov 20, 2018 - [change log at github]
topolink-18.284.tar.gz Released on Oct 11, 2018 - [change log at github]
topolink-18.269.tar.gz Released on Sep 26, 2018 - [change log at github]
topolink-18.263.tar.gz Released on Sep 20, 2018 - [change log at github]
topolink-18.229.tar.gz Released on Aug 17, 2018 - [change log at github]
topolink-18.226.tar.gz Released on Aug 14, 2018 - [change log at github]
topolink-18.200.tar.gz Released on Jul 19, 2018 - [change log at github]
topolink-18.198.tar.gz Released on Jul 17, 2018 - [change log at github]
topolink-18.181.tar.gz Released on Jun 30, 2018 - [change log at github]
topolink-18.170.tar.gz Released on Jun 19, 2018 - [change log at github]
topolink-18.158.tar.gz Released on Jun 07, 2018 - [change log at github]
topolink-18.128.tar.gz Released on May 08, 2018 - [change log at github]
topolink-18.127.tar.gz Released on May 07, 2018 - [change log at github]
topolink-17.332.tar.gz Released on Nov 28, 2017 - [change log at github]
topolink-17.331.tar.gz Released on Nov 27, 2017 - [change log at github]
topolink-17.131.tar.gz Released on May 11, 2017 - [change log at github]
topolink-17.130.tar.gz Released on May 10, 2017 - [change log at github]
topolink-17.125.tar.gz Released on May 05, 2017 - [change log at github]
topolink-17.069.tar.gz Released on Mar 10, 2017 - [change log at github]
topolink-17.010.tar.gz Released on Jan 10, 2017 - [change log at github]
topolink-16.362.tar.gz Released on Dez 27, 2016 - [change log at github]
topolink-16.354.tar.gz Released on Dec 19, 2016 - [change log at github]
topolink-16.351.tar.gz Released on Dec 16, 2016 - [change log at github]
topolink-16.348.tar.gz Released on Dec 13, 2016 - [change log at github]
topolink-16.343.tar.gz Change log
topolink-16.341.tar.gz Release 16.341
topolink-16.333.2.tar.gz Release 16.333.2
topolink-16.333.tar.gz Release 16.333
topolink-16.330.2.tar.gz Release 16.330.2
topolink-16.330.tar.gz Release 16.330
topolink-16.323.tar.gz Release 16.323
topolink-16.281.tar.gz Added pdbfile to input example and changed the input file example.
topolink-16.278.tar.gz Added error message if link dir does not exist.
topolink-16.264.tar.gz Update version.
topolink-16.263.tar.gz Added linkensemble program.
topolink-16.253.tar.gz Stable version with evalmodels and linkcorrelation analysis programs.
topolink-16.230.tar.gz Improved reading of input files containing TAB characters. Fixed reading of H atoms.
topolink-16.176.tar.gz updated title file for versioning
topolink-16.168.tar.gz Updated Makefile with devel option.
topolink-16.146.tar.gz Added spaces after results in final output
topolink-16.083.tar.gz Added error message if observed, linktype and deadend keywords are found outside experiment section.
topolink-16.082.2.tar.gz Removed .git directory uploaded by error to version history.
topolink-16.082.tar.gz Removed object files uploaded by error.
topolink-16.081.3.tar.gz Makefile creates bin directory.
topolink-16.081.2.tar.gz Added the scorecut option for considering only best observed crosslinks.
topolink-16.081.tar.gz Added title.f90 file for cleaner upload to git.
topolink-16.079.tar.gz Reads score field for each observed crosslink, and computes overall experiment score.
topolink-16.078.tar.gz Added checking of missing atoms in PDB.
topolink-16.061.2.tar.gz Fixed bug on computing linkstatus when reading from previous log.
topolink-16.061.tar.gz Fixed output of LINK line.
topolink-16.029.tar.gz Added final statistics for all experiments, and improved status definition.
topolink-16.028.tar.gz Reads previous log and various fixes. Development version.
topolink-16.027.tar.gz New definitions for likelihood and other fixes.
topolink-16.026.tar.gz Object-oriented version, with experiment-dependent likelihood computation.
topolink-16.015.tar.gz Various fixes.
topolink-16.012.tar.gz New version perhaps ready. Needs testing.
topolink-16.011.tar.gz Version with multiple experiments, appears to work (beta)
topolink-16.008.tar.gz Reformulated for multiple experiments and computing number of inconsistencies (beta)
topolink-16.007.tar.gz Counts a valid observed link only if d<=dmin
topolink-16.006.2.tar.gz Improved output formatting
topolink-16.006.tar.gz Improved error messages.
topolink-15.352.tar.gz Changed the definition of the likelihood for automatic computing incorrect probability.
topolink-15.294.tar.gz Fixed printing of wrong best link and added additional reading options.
topolink-15.293.tar.gz Added chain descriptors for links and residues, and other changes.
topolink-15.286.tar.gz Changed the way of computing likelihood and prints also its log
topolink-15.282.tar.gz First version online.