eSimDock Datasets

eSimDock is a similarity-based approach to ligand docking and binding affinity prediction. Given the receptor structure, anchor ligand and a query compound, it employs machine learning and a set of physics-based as well as statistical potentials to predict the binding pose and estimate the corresponding binding affinity.
csb03
If you use eSimDock, please cite the following paper:

eSimDock is available as a webserver. See the manual for instructions on how to use the webserver as well the details on the output file format.

eSimDock uses AutoDock Vina, Balloon, DrugScore, KCOMBU, LIBSVM, LIGPLOT, LPC, MayaChemTools, MGLTools, and OpenBabel.

eSimDock 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, docking ligands as well as the docking results from eSimDock v1.0.

Astex/CCDC
Dataset Download Size MD5  

 
Receptor crystal structures astex-receptor-crystal.tar.gz 8.8M 3b587a1b89398264eba27427d0aea75d  
Ligands for crystal structures astex-ligand-crystal.tar.gz 2.8M 4528b2df1abc272c114ef8474311b200  
Receptor distorted structures astex-receptor-distorted.tar.gz 88M 1f3cf89f8dca7837562c937d8f1318e5  
Ligands for distorted structures astex-ligand-distorted.tar.gz 28M 450a0a92697ac42b7c74fcaef7150791  
Anchors derived by eFindSite astex-anchor-efindsite.tar.gz 71M a0949c883a859ce578ee6e779bf0c0ec  
Docking against crystal structures astex-esimdock-crystal.tar.gz 145k 858f6933217b9404f1050852245dc7ce  
Docking against distorted structures astex-esimdock-distorted.tar.gz 1.5M e7695912bae9fa720a9193f8dec87b1e  
Docking using eFindSite anchors astex-esimdock-efindsite.tar.gz 419k 3eaf24609dbdb7543ebc8ff2296a0fa6  
BindingDB
Dataset Download Size MD5  

 
BindingDB compounds bindingdb-compound.tar.gz 13M 2336c8a972ed4cba60108e71791a4037  
ZINC decoys bindingdb-decoy.tar.gz 291M 6e9d82be970a89ea30cb58e058e92ecc  
Receptor crystal structures bindingdb-receptor-crystal.tar.gz 47M 1f3bff6913e5b4734b64d89275674cc2  
Anchors for crystal structures bindingdb-ligand-crystal.tar.gz 799k 98de26225a3901a496339a893f8b852b  
Receptor distorted structures bindingdb-receptor-distorted.tar.gz 277M a91ca6210eec2fa2db052742843432e1  
Anchors for distorted structures bindingdb-ligand-distorted.tar.gz 5.1M e0e893b5738f5a2fd806869f2425c4f2  
Docking against crystal structures bindingdb-esimdock-crystal.tar.gz 630k 49a85a89914e96630a850a16ef0ef180  
Docking against distorted structures bindingdb-esimdock-distorted.tar.gz 3.8M d2448ea5bbe60f2688cc90960bb15e7e  
Docking of decoy compounds bindingdb-esimdock-decoy.tar.gz 17M 49eab60f04f74a3003159a34d245a06a  
fXa
Dataset Download Size MD5  

 
Receptor structure fXa-receptor.pdb.gz 30k d529ab5f5d6fdd3f27c81f1280ba8fb3  
Anchor substructures fXa-anchor.sdf.gz 56k 8c0d917326788f47f8b0b79691bcb26e  
Training subset of binders fXa-training_set.sdf.gz 4.6M 1ed207ab1835f26029392d8d85879b22  
Validation subset of binders fXa-validation_set.sdf.gz 2.3M c4681f1aaf7fd4d876964c8e43c91704  
Docking of training compounds fXa-esimdock-training_set.sdf.gz 176k 7874a560a6d71aeb41b84bf70bbb3f98  
Docking of validation compounds fXa-esimdock-validation_set.sdf.gz 90k 9fb4ff38f26ab6d238d30bb1cabfac07  
CDK2
Dataset Download Size MD5  

 
Receptor structure cdk2-receptor.pdb.gz 38k 2cbb2980a610055ea97f59e1fe7f3f3e  
Anchor substructures cdk2-anchor.sdf.gz 380k 5dd0a431f94c58c1465ad46791ed1768  
Known inhibitors cdk2-inhibitors.sdf.gz 9.3M 4d2e61868c3afeb82e241b927de145f7  
Docking of inhibitors cdk2-esimdock.sdf.gz 443k ae535ec5341f2b81bbac31c493959e9e  

 

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