Software, Documentation, and Examples

Licensed users may download software distributions and updates below. Software distributions include binary executables for Windows, Linux, and Mac platforms. The modules of the Surflex Platform are being integrated with multiple modeling front-ends to enhance ease-of-use. Software distributions are gzip compressed tar archives. Installation involves unpacking the archive and ensuring that your licensing file is in the right place.

Surflex v5.1

Surflex v5.0

Surflex v4.5 (revision 3)

Surflex v4.5 (revision 2)

The Surflex Manual has detailed instructions for installation and extensive examples of use of all four modules.

 

Release Notes

v5.101: This is a minor version update, primarily to introduce the xGen module. If a user is licensed for the Docking module, then the xGen module will also be available. The example set has been updated for the current binaries on the reference Linux platform.

v5.001: This is the initial release of Surflex Platform Version 5. The primary changes are as follows:

  • The Tools module includes improvements in ligand Kekulization, constrained minimization, and constraint-based conformer search. Default behavior has changed for heuristic protonation (heuristic protonation is turned on by default rather than assuming that formal charges in .smi or .sdf files are intended by the user).
  • The QuanSA module incorporates improvements in the manner in which crystallographic data can be used to guide model building as well as improvements in the model refinement process when adding new training molecules.
  • The Sim module contains improvements in multiple-ligand alignment.
  • The Docking module now implements a blended approach to electrostatics, combining a Coulombic approach with the pre-existing directional hydrogen-bonding method, and the eSim method has been integrated into the docking process and pose family generation process.

The full set of examples have been run with the v5.001 Linux binary on the reference platform.

 

Non-Commercial Academic Research Licensing

The free academic version is unsupported and is available for users at qualifying academic or non-profit research institutions within the United States and for qualifying users within the following countries, all of which are active members within the Organization for Economic Co-operation and Development: Australia, Austria, Belgium, Canada, Denmark, Finland, France, Germany, Greece, Ireland, Italy, Japan, Luxembourg, Netherlands, New Zealand, Norway, Poland, Portugal, Slovenia, South Korea, Spain, Sweden, Switzerland, and United Kingdom. Restriction to these countries is driven by intellectual property considerations.

The software will be made available pending execution of a licensing agreement, which is accessed via download. The form must be filled out in its entirety using PDF reading software, printed, signed, scanned, and then emailed to the address on the form. Completed licenses are reviewed approximately four times per year. Note that the “Licensee” is the academic or non-profit institution in which the Surflex software will be used (NOT the individual making the request). The individual signing the licensing agreement must be authorized to make such agreements on behalf of their institution (typically faculty-level individuals have such authority but students and post-docs do not). Those that meet criteria are signed and archived, with the lab contact receiving a license key via email. Those that fail to meet criteria (e.g. non-qualifying institution or illegible/missing information on the form) will generally receive no explicit notification.