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 v5.190 (minor binary-only update to v5.189: Release Notes)

Surflex v5.189 (minor update, full release with examples)

Surflex v5.186 (minor update, full release with examples)

Surflex v5.173 (minor update, full release with examples)

Surflex v5.164 (minor binary update)

Surflex v5.162 (minor update, full release with full examples)

Surflex v5.142 (minor update, full release with full examples)

Surflex v5.137 (minor binary update)

Surflex v5.125 (minor update, full release with full examples)

Surflex v5.114 (patch binaries for minor bug fixes)

Surflex v5.111

Surflex v5.1

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

 

Brief Release Notes (see detailed Release Notes for more information)

v5.173-v5.189: Minor bug fixes and improvements.

v5.162: Minor bug fixes and improvements.

v5.142: Minor bug fixes and improvements.

v5.137: Minor bug fixes and improvements.

v5.125: Added new utility functionality to the Tools module for deeper conformational search of complex molecules. Minor bug fixes and improvements in other modules.

v5.111: Added new utility functionality to the Tools module for analysis and manipulation of conformer ensembles. Added multi-core capabilities for PSIM and GrindPDB operations. Improved ligand protonation and kekulization.

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.

 

Non-Commercial Academic Research Licensing

A deeply discounted (roughly 85%) academic license may be 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 formal licensing agreement, which will specify whether the license is for use across an institution, a department, or a single laboratory. Due to the variability across academic/non-profit institutions, each case will be considered based on the specifics involved. Pricing will be dependent on the breadth of usage that is licensed. No formal support is offered with discounted academic/non-profit licenses. Interested parties should contact academic_license@biopharmics.com.