eMatchSite Datasets

eMatchSite is a sequence order-independent algorithm for ligand binding site alignment and matching. It accurately identifies pairs of pockets that bind similar compounds even in proteins with different global structures. Furthermore, it tolerates structural distortions in protein models, thus experimentally solved structures are not required.
csb12
If you use eMatchSite, please cite the following paper:

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

eMatchSite is free of charge under the terms of GNU General Public License for the general public and under a dual license for commercial users.



Below, you can find benchmarking datasets as well as the output files generated by eMatchSite v1.0. Note that templates with >40% sequence identity to the target were excluded from the benchmark calculations.

SOIPPA
Dataset Download Size MD5  

 
Protein crystal structures soippa-protein-crystal.tar.gz 13M ca62a95f1c29f2ace1e2828c9811df40  
Protein distorted structures soippa-protein-distorted.tar.gz 37M b493794331121753ea184087a55f42fb  
Protein models soippa-protein-model.tar.gz 25M a091a35ec125bdf2b17fddd00b161274  
Ligands for crystal structures soippa-ligand-crystal.tar.gz 338k 14ad44d0ddd4b86d12e633d569297e79  
Ligands for distorted structures soippa-ligand-distorted.tar.gz 1.0M bbcce8d4ff439c963b3e9cc18536e89e  
Ligands for protein models soippa-ligand-model.tar.gz 708k 232c7b68baa2819f880f7eb3883c2474  
eFindSite data for crystal structures soippa-efindsite-crystal.tar.gz 1.2G de41cd551687994a8c9477750ee578c0  
eFindSite data for distorted structures soippa-efindsite-distorted.tar.gz 3.3G 6f0ee1025e2a4be10b83e7a935e32c31  
eFindSite data for protein models soippa-efindsite-model.tar.gz 2.3G 77302bb96d1d90e0b2e5ad34ee325054  
eMatchSite output for crystal structures soippa-ematchsite-crystal.tar.gz 672M 7f8b0046b9817207d85c17c1d4b65004  
eMatchSite output for distorted structures soippa-ematchsite-distorted.tar.gz 1.8G ecc45549664703b15a4060103eff787d  
eMatchSite output for protein models soippa-ematchsite-model.tar.gz 1.2G cfb2b674c976ec89dfddeec153a97e9f  
Homogeneous
Dataset Download Size MD5  

 
Protein crystal structures homogeneous-protein-crystal.tar.gz 3.4M 01e53fe5a5a2b7a9721ec254bc217946  
Protein models homogeneous-protein-model.tar.gz 6.7M 9ba99ea67992df140c846f26976db6f7  
Ligands for crystal structures homogeneous-ligand-crystal.tar.gz 77k 36d0f27bdada83c94831a07519a640e0  
Ligands for protein models homogeneous-ligand-model.tar.gz 160k 2fb39a28c0e4822e2c5d81232795a431  
eFindSite data for crystal structures homogeneous-efindsite-crystal.tar.gz 292M 57173ad27cbd5dfe65e1def2ad5daa67  
eFindSite data for protein models homogeneous-efindsite-model.tar.gz 570M 00c4c0f9b607c82c6d94d8b236d64d80  
eMatchSite output for crystal structures homogeneous-ematchsite-crystal.tar.gz 47M accfdcec838a1d81cba160a2c2f5c779  
eMatchSite output for protein models homogeneous-ematchsite-model.tar.gz 54M cee39c291d76c93af373535ab9b39fbd  
Kahraman
Dataset Download Size MD5  

 
Protein crystal structures kahraman-protein-crystal.tar.gz 3.5M a734591ba59e7f6312dfe0c687fae3b0  
Protein models kahraman-protein-model.tar.gz 6.9M e4c5bd4d5d0f1f8722970c9bb3207c35  
Ligands for crystal structures kahraman-ligand-crystal.tar.gz 110k 1e96db92e58d3135ab2662da18206648  
Ligands for protein models kahraman-ligand-model.tar.gz 230k b43afd9c33e48a253dc4e9a913f2bdbc  
eFindSite data for crystal structures kahraman-efindsite-crystal.tar.gz 215M 0d636e13509453fa5de1ecab835ff8cf  
eFindSite data for protein models kahraman-efindsite-model.tar.gz 409M 12142740f040c04d68faaab1dd98ddd2  
eMatchSite output for crystal structures kahraman-ematchsite-crystal.tar.gz 52M 1dc16c890df7aa21efe20c04e94dcc3f  
eMatchSite output for protein models kahraman-ematchsite-model.tar.gz 82M ed6f8fb348401371163d8b3dbbddd973  
Steroid
Dataset Download Size MD5  

 
Protein crystal structures steroid-protein-crystal.tar.gz 63M 3052c6688070d91dd7fe7ab6c30e8566  
Protein models steroid-protein-model.tar.gz 126M 4e83d6f072221e332c9b6bc40a34daa9  
Ligands for crystal structures steroid-ligand-crystal.tar.gz 1.7M 6b28fa13447db212487dd3db15468822  
Ligands for protein models steroid-ligand-model.tar.gz 3.5M 161f1e33e8d8c6c8bbec3b3a34344b01  
eFindSite data for crystal structures steroid-efindsite-crystal.tar.gz 6.4G 2e935508d10149eb1ad77e3985ff9a61  
eFindSite data for protein models steroid-efindsite-model.tar.gz 13G 2c4d0f3a1041f0a1c88244ea15026d14  
eMatchSite output for crystal structures steroid-ematchsite-crystal.tar.gz 465M f5550d363391c7d52707dd15facc7595  
eMatchSite output for protein models steroid-ematchsite-model.tar.gz 733M 672be0e094e3c7eff1b9f1265e78a5aa  

 

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