What's New

November 17, 2011
We have released Surflex version 2.6. The primary changes involve the inclusion of computations for protein pocket similarity (accessed through Surflex-Dock) and for computing log-odds scores of molecules compared with sets of other molecules. These new functions are described in two recent papers (see the Publications tab).

November 10, 2010
We have released Surflex version 2.5. The primary changes are under the hood, but there are significant speed increases, particularly in Surflex-Sim for virtual screening. Typical screening times per molecule, using a single query ligand, are less than one second on the fastest setting (-fscreen) and approximately one second on the standard screening parameters (-pscreen).

September 15, 2010
We have just published a paper addressing a fundamental limitation of most QSAR methods: their lack of physically meaning. By constructing physical active sites for ligand affinity prediction, not only can our QMOD approach produce accurate predictions of affinity and binding mode, it can do so in cases where structure-activity relationships are highly non-additive (see Publications).

March 9, 2010
Dr. Jain is pleased to deliver the OpenEye CUP XI Annual Levinthal Lecture: Molecular Evolution: The Created and the Creators and the Puzzle of Design.

October 24, 2009
We have published two new papers (see Publications tab). The first addresses docking with protein flexibility, and the second introduces a new method to construct binding site models de novo from ligand activity data. The Surflex software corresponding to the first publication is v2.415, now available. The software corresponding to the second paper is still pending release.

December 16, 2008
We have released Surflex Version 2.4, which incorporates the custom scoring function tuning methods decribed in Pham and Jain (2008). This version also includes support for docking to multiple protein conformations. Within the similarity module, additional options have been added to parallel developments with Surflex-Dock. In particular, a new option for fast screening (-fscreen) yields significantly faster times for ligand-based virtual screening.

February 5, 2008
Two methodological papers have been published in a special issue of the Journal of Computer-Aided Molecular Design that relate to methodological performance testing (see the Publications tab). An additional paper describing a method for customization of scoring functions has been published separately. A minor version release of Surflex (v2.2) corresponds to these papers and is available to academic users for download.

April 17, 2007
We have added a Mac version of the Surflex tools to the current (v2.11) distribution. Academic users of the Surflex package may re-download the distribution to gain access. Note that Surflex, fully integrated with SYBYL, is available for commercial use through Tripos Inc. Academics may also obtain a supported and integrated version through Tripos at a substantial discount. The free academic version is unsupported, but we do like to hear about experiences and receive reports of unusual program behavhior (see the Contact tab for an email address).

March 1, 2007
We are pleased to announce the publication of a major new version of Surflex-Dock in the Journal of Computer-Aided Molecular Design (see the Publications tab). The new version, fully integrated with SYBYL, is available for commercial use through Tripos Inc. Academics may also obtain a supported and integrated version through Tripos at a substantial discount. An unsupported academic version is available as well (please see the Contact tab for an email address).