About

SwissDock is a web service that predicts the molecular interactions likely to occur between a target protein and a small molecule. On SwissDock 2, two docking methods can be used: When using AC, the rough energy landscape of the macromolecule is replaced by a smooth attracting energy landscape generated by virtual attracting points surrounding the macromolecular surface. Then the sampling algorithm for docking is constituted of simple rotations, translations and geometry optimizations of the ligand in the smooth landscape. Optimizations in the "mold" are followed by optimizations in the actual protein energy landscape and an implicit solvation treatment. The scoring function of AC is composed of the CHARMM force field terms and the fast analytical continuum treatment of solvation (FACTS) model.

The Vina scoring function comprises a potential like van der Waals forces, an undirected hydrogen-bond component, a hydrophobic factor, and a penalty for conformational entropy. Vina computes interactions between molecules through trilinear interpolations of precalculated grid maps on the target structure, and it uses the target structure for postprocessing minimization of the docked poses.


Attracting Cavities 3.0

Attracting Cavities 3.0 is now available for download under the following license:

Licensed Work: Attracting Cavities version 3
Licensor: Molecular Modelling Group of the Swiss Institute of Bioinformatics
Change Date: 2030-01-01
Change License: GPL v3

Additional Use GrantPermitted Uses:
  • Personal research use
  • Academic research use
  • Educational use
  • Internal business use
Restrictions:
  1. Redistribution Prohibited

    2. The Licensed Work, in original or modified form, may not be redistributed, sublicensed, or shared with third parties without prior written permission from the Licensor.

  2. Commercial Use Prohibited

    3. The Licensed Work may not be sold or licensed for a fee.

  3. Competing Services Prohibited

    4. The Licensed Work may not be used to create, operate, support, or provide any web service, server, platform, or software system competing with SwissDock, whether commercial or non-commercial.

  4. Publication Citation Requirement

    5. Any publication, presentation, report, or public disclosure containing results generated using the Licensed Work must appropriately cite the following publications:

    1. Röhrig UF, Mathieu-Bugnon M, Zoete V. Attracting Cavities 3.0: faster and more versatile molecular docking for the SwissDock webserver. Bioinformatics, 2026, ASAP

    2. Röhrig UF, Goullieux M, Bugnon M, Zoete V. Attracting Cavities 2.0: improving the flexibility and robustness forsmall-molecule docking. J. Chem. Inf. Model., 2023, 63 (12), 3925–3940, DOI: 10.1021/acs.jcim.3c00054

    3. Zoete V, Schuepbach T, Bovigny C, Chaskar P, Daina A, Röhrig UF, Michielin O. Attracting Cavities for Docking. Replacing the Rough Energy Landscape of the Protein by a Smooth Attracting Landscape. J. Comput. Chem., 2016, 37 (4), 437–447. DOI: 10.1002/jcc.24249

  5. Modification

    6. Users may modify the Licensed Work for their own permitted internal use, but modified versions remain subject to all terms of this License.

Effective on the Change Date, this license will convert to GPL v3.

This program uses the external program CHARMM (https://www.academiccharmm.org/), subject to its own license terms.

Click here to download Attracting Cavities 3.0.


Disclaimer

See terms of use.