eFindSite Datasets

eFindSite is a ligand binding site prediction and virtual screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins identified by 10 threading/fold recognition methods.
If you use eFindSite, please cite the following papers:

eFindSite is available as a webserver and a standalone software distribution. See the manual for the details on the output file format.

eFindSite uses the following compound libraries:


eFindSite is free of charge under the terms of GNU General Public License for non-commercial use. It is distributed without any warranty, but with best wishes.

Below, you can find the non-redundant sets of target structures, the list of templates used for function annotation as well as the output files generated by eFindSite v1.0. Note that templates with >40% sequence identity to the target were excluded from the benchmark calculations.

Target proteins (PDB dataset)
Dataset Download Size MD5  

Target crystal structures crystal-structures.tar.gz 113M 7a83d640f0c479c023891092d346220e  
High-quality target models models-high.tar.gz 113M 7d31cdf2885cf45c527176efae9ef10d  
Moderate-quality target models models-moderate.tar.gz 113M 0c667919045c24942ebf062218cc7ceb  
Other input files (PDB dataset)
Dataset Download Size MD5  

Templates identified by eThread target-ethread-fun.tar.gz 20M caaa2efefab78ff39b18e0a0c92570a1  
Target sequence profiles target-profiles.tar.gz 52M 3b155a85e28b39eb8a3b04d8779c20a8  
Secondary structure by PSIPRED target-psipred.tar.gz 7.4M 351d5b52407d1b023439e7c7a52e8476  
eFindSite predictions (PDB dataset)
Dataset Download Size MD5  

Target crystal structures efindsite-crystal-structures.tar.gz 14G 3c190c12d39e015327ae3a4f164d3ec0  
Target crystal structures
+ auxiliary ligands
efindsite-crystal-structures-lig.tar.gz 14G 2d26b3a73ba53b0557c5310fcd621702  
High-quality target models efindsite-models-high.tar.gz 14G 73dae45a5f8ffbf84e093c4c8d41c8d2  
High-quality target models
+ auxiliary ligands
efindsite-models-high-lig.tar.gz 14G d08b8fcc52b8de85d72426032a8216d7  
Moderate-quality target models efindsite-models-moderate.tar.gz 14G 60b1f4aa0e5ebc185eb77462f59ed338  
Moderate-quality target models
+ auxiliary ligands
efindsite-models-moderate-lig.tar.gz 14G 3815e37cb3bf806056a3c16ff7eea8de  
Target protein data (DUD-E dataset)
Dataset Download Size MD5  

Target crystal structures dud-e.data-crystal-structures.tar.gz 9.1M 621f3e3dba747034d7d66f8d426e4a6a  
High-quality target models dud-e.data-models-high.tar.gz 9.1M 611b1437fc506c97dbd3721a67c89a45  
Moderate-quality target models dud-e.data-models-moderate.tar.gz 8.5M 5d883106fd2c7cb3aa48934424fe8372  
eFindSite predictions (DUD-E dataset)
Dataset Download Size MD5  

Target crystal structures dud-e.efindsite-crystal-structures.tar.gz 406M a94e6006f033fe7d2562016dae667663  
High-quality target models dud-e.efindsite-models-high.tar.gz 373M a7b903b8071c7057ef9e9d5dad24b1c0  
Moderate-quality target models dud-e.efindsite-models-moderate.tar.gz 339M 34ee69c312704d74e00ca4dfe956c084  
Compound libraries (DUD-E dataset)
Dataset Download Size MD5  

Actives (for use with eFindSite) dud-e.lib-actives.tar.gz 3.1M e1974cb0b66061633c0945406e07784c  
Decoys (for use with eFindSite) dud-e.lib-decoys.tar.gz 173M a9b3cbf50d973b3babb6bf0226bb56c4  
Compounds ranked by eFindSite (DUD-E dataset)
Dataset Download Size MD5  

Target crystal structures dud-e.ranking-crystal-structures.tar.gz 14M 007b8da4afbf572f77da1645701b30be  
High-quality target models dud-e.ranking-models-high.tar.gz 13M c040e2dce6e232492f1859772552e9ad  
Moderate-quality target models dud-e.ranking-models-moderate.tar.gz 12M 3f1d6f6c64f8c99534cee2f77c05829f  


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