Software Download

Please find below a list of software available from this website. Links to manuals are provided in the table.

The maintenance status differs between packages. The license below implies no support or liability of any type.

Most of our recent tools, including input scripts and data for specific publications can be found in our lab's public GitLab repository. This includes the latest version of SEED, which we recommend obtaining from there rather than from the link below (which is infrequently updated).

Note that the Caflisch lab has also been involved in the development of software packages hosted elsewhere, most notably CHARMM, CAMPARI, and Wordom. You can find web links to these packages along with further information also under Miscellanea.

Please read the license agreement carefully before submitting a download request.

Short description Manual File (Version) Reference Publication

Automatic chemical space expansion through virtual coupling of compounds (AutoCouple). The code is freely available at https://github.com/Caflisch-Group/AutoCouple_Python-based (latest version posted March 26 2019).

 Chemical space expansion of bromodomain ligands guided by in silico virtual couplings (AutoCouple)

CAST or CHARMm Atom Assignment is a command-line tool to assign (TAFF) atom types to molecules in .mol2 format (latest version is 0.1 posted November 16 2011).

 PDF icon CAST_help.pdf cast_v.0.1.tgz unpublished results

DAIM stands for Decomposition And Identification of Molecules (latest release is version 5.3 posted Nov 14 2010).

 PDF icon daim.pdf daim-5.3_send.tgz Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking

FFLD stands for Fragment-based Flexible Ligand Docking and the latest version is 3.3 (posted March 30 2009).

 PDF icon ffld.pdf ffld_send_3.3.tgz Fragment-based flexible ligand docking by evolutionary optimization

FLEA clusters output poses of FFLD with a Leader algorithm. The latest version is 1.0 (posted May 30 2014).

 PDF icon flea_manual.pdf FLEA_dist_64bit.tgz unpublished results

GANDI stands for Genetic Algorithm-based de Novo Design of Inhibitors. It links docked fragments and the latest release is 2.0 (posted July 02 2014).

 PDF icon gandi.pdf gandi_2.0.tgz Fragment-based de novo ligand design by multiobjective evolutionary optimization

SEED (Solvation Energy for Exhaustive Docking) is a program for docking libraries of fragments (latest release is 4.0.0 posted October 20, 2017). SEED is open-source software. The latest release and the development version can be freely downloaded from https://gitlab.com/CaflischLab/SEED.
The online documentation of SEED is hosted at https://caflischlab-seed.readthedocs.io/en/latest.

 PDF icon seed_4.0.0_doc.pdf Efficient electrostatic solvation model for protein-fragment docking

VLG or Virtual Library Generator is a tool for generating compounds by adding substituents to a scaffold. The latest version is 1.0 (posted August 31 2009).

PDF icon vlg.pdf VLG.tgz unpublished results

Wit!P is a molecular graphics and modeling tool originally developed by Armin Widmer at Novartis. Note that the documentation is outdated in parts (latest release posted July 2 2014).

 Package icon Witnotp_html.zip wnpexp-20140618.tgz unpublished results

License Agreement

The recipient agrees not to disclose in any form either the delivered software package (package) or any modifications or derivative works based on the package to any third parties.

The recipient agrees that it will use the package solely for internal purposes.

The recipient agrees that any reports or publication of results obtained with the package will acknowledge its use by an appropriate citation. Until further notice this would refer to the package and to the relating papers of A. Caflisch group. The authors of the package or the University of Zurich make no warranties, either expressed or implied, as to the fitness of the program for any particular purpose, nor shall they be liable for any direct, indirect, or other damage resulting from use of the program. No particular support, service or update of the package is implied as part of the agreement. However technical contacts and advice are granted on a voluntary, friendly basis.

Please note that the Wit!P version distributed here is subject to a separate BSD 3-clause. All other software is licensed under the terms listed above.

 

Source code will be provided by personal request only and is not generally included with the packages available for download through the form below.

 

Sincerely yours,
Amedeo Caflisch

Software Download Request

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