Software
The Surflex Platform software is available via BioPharmics LLC.
Data Sets
All interested parties are welcome to download benchmarking data as well. The benchmarking data files are listed below according to the paper in which results were presented. Note that the scripts for the benchmarks are not updated for minor version changes and require minor editing to specify the correct binary executable. Please also note that if an archive is not listed below for a particular paper, it may be a rare case where we have made use of proprietary data from a collaborator and are not free to release the data, or the data may be part of a benchmark maintained by another group, or the archive may be so large as to make web-hosting infeasible. Please inquire via email in such cases.
Jain/Cleves/Walters DiffDock Archive 2024
Cleves/Tandon/Jain PINC+Macro Surflex-Dock Archive 2024
Cleves/Jain/Hancock UK2A-Adavelt Archive 2024
Jain/Mueller PD-L1 Macrocycle Optimization Archive 2023
Williamson/Jain Rapamycin Archive 2023
Jain/Sherer Strain Archive 2023
xGen Peptide Strain Archive 2021
DUD-E+ eSim Pose Prediction Benchmark
DUD-E+ (rev1) JCAMD 2019/2020 eSim and Surflex-Dock Benchmark
ForceGen JCAMD 2019 Conformer Generation Benchmark
Cleves/Jain JCAMD 2015 PINC Cross-Docking Data
Cleves/Jain JCAMD 2015 Polypharmacology Data
Yera/Cleves/Jain PSB 2014 Test Data
Jain JCAMD 2010 Test Data (QMOD2)
Langham/Jain JMedChem 2009 Test Data (QMOD)
Jain JCAMD 2009 Test Data (Protein Flexibility)
Pham/Jain JCAMD 2008 Test Data (Custom Scoring)
Cleves/Jain JCAMD 2008 Test Data (Inductive Bias)
Jain JCAMD 2008 Test Data (Docking Eval)
Jain JCAMD 2007 Test Data (Surflex-Dock 2.1)
Pham/Jain JMedChem 2006 Test Data (rev1)
Cleves/Jain JMedChem 2006 Test Data