| Name | Type | Description | Added | Edit |
|---|
| PDBbind15PlcSample | Molecules | The aim of the PDBbind database is to provide a comprehensive collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB). It thus provides an essential linkage between energetic and structural information of these complexes, which is helpful for various computational and statistical studies on molecular recognition occurred in biological systems. | 2016-05-19 20:25:00 | Delete |
| ScorePDBbind14RefTrTs | Descriptors | This data is the 2014 refined set of PDBBind protein-ligand complexes characterized by sixteen different descriptor sets. The data also includes experimental binding affinities collected from the literature by the curators of PDBbind. This data set is ideal for training and evaluating machine-learning scoring functions for the tasks of binding affinity prediction and ligand ranking. It is composed of 3446 protein-ligand complexes characterized by more than 2700 descriptors from 16 different scoring functions and interaction modeling tools. | 2016-05-20 08:18:05 | Delete |
| ScorePDBbind14PrTr | Descriptors | This data is the 2014 primary training set of PDBBind protein-ligand complexes characterized by sixteen different descriptor sets. The data also includes experimental binding affinities collected from the literature by the curators of PDBbind. This data set is ideal for training machine-learning scoring functions for the tasks of binding affinity prediction and ligand ranking. It is composed of 3251 protein-ligand complexes characterized by more than 2700 descriptors from 16 different scoring functions and interaction modeling tools. The primary training set is a subset of the refined set of PDBbind 2014. (The refined set can be found in DDB under the name ScorePDBbind14RefTrTs.) | 2016-05-20 08:25:32 | Delete |
| ScorePDBbind14CrTs | Descriptors | This data is the 2014 core test set of PDBBind protein-ligand complexes characterized by sixteen different descriptor sets. The data also includes experimental binding affinities collected from the literature by the curators of PDBbind. This data set is ideal for testing machine-learning scoring functions for the tasks of binding affinity prediction and ligand ranking. It is composed of 195 protein-ligand complexes grouped into 65 clusters of protein families. The size of each cluster is three complexes in which the three ligands bind to the same protein but with very different binding affinity values. The complexes are characterized by more than 2700 descriptors from 16 different scoring functions and interaction modeling tools. The testing data ScorePDBbind14CrTs is a subset of the refined complexes of the PDBbind 2014 and it can be used for testing ML SFs that were trained on the non-overlapping primary training set ScorePDBbind14PrTr (its DDB name). | 2016-05-20 08:40:13 | Delete |
| XANLDRSADGC_xgboost | SF | This is an XGBOOST based SF fitted to the Primary set of 2014 PDBbind and tested on the core set of the same PLC database. | 2016-05-20 08:44:55 | Delete |
| XANLDRSADGC_filter | Filter | This is a filter that was built to detect noisy descriptors derived using 11 different tools. | 2016-05-20 08:53:28 | Delete |
| ScorePDBbind15CrTs | Molecules | This data is the 2015 core test set of PDBBind protein-ligand complexes characterized by sixteen different descriptor sets. The data also includes experimental binding affinities collected from the literature by the curators of PDBbind. This data set is ideal for testing machine-learning scoring functions for the tasks of binding affinity prediction and ligand ranking. It is composed of 195 protein-ligand complexes grouped into 65 clusters of protein families. The size of each cluster is three complexes in which the three ligands bind to the same protein but with very different binding affinity values. The complexes are characterized by more than 2700 descriptors from 16 different scoring functions and interaction modeling tools. The testing data ScorePDBbind14CrTs is a subset of the refined complexes of the PDBbind 2015 and it can be used for testing ML SFs that were trained on the non-overlapping primary training set ScorePDBbind14PrTr (its DDB name). The 2014 and 2015 PDBbind core test sets are identical. | 2016-05-20 09:07:47 | Delete |
| nnscoreSminaDpocketDescs | Descriptors | The descriptor types that might include descriptors for protein targets only | 2016-05-26 06:29:04 | Delete |
| allDescriptors_Xgboost_Pr14Cr14 | SF | Xgboost fitted to Pr14 characterized by all descriptors and tested on Cr14 | 2016-05-26 07:09:24 | Delete |
| allDesc_BRT | SF | BRT on all descriptors Pr14/Cr14 | 2016-05-26 07:46:25 | Delete |
| XGBOOST_with_shuffle | SF | | 2016-05-26 22:06:27 | Delete |
| dnn_xag1030 | SF | | 2016-11-08 03:31:32 | Delete |
| many1036 | SF | | 2016-11-08 03:40:40 | Delete |
| svm1102 | SF | | 2016-11-08 04:02:51 | Delete |
| test_file | Descriptors | test_descript | 2017-06-16 17:41:51 | Delete |
| -d | Descriptors | | 2017-10-31 03:06:05 | Delete |
| -d | Descriptors | | 2018-01-04 03:50:32 | Delete |
| ID1 | Descriptors | | 2018-01-04 15:29:48 | Delete |
| -u | Filter | | 2018-01-16 18:55:41 | Delete |
| -u | Filter | | 2018-01-16 19:57:27 | Delete |
| -d | Descriptors | | 2018-01-17 14:34:00 | Delete |
| -d | Descriptors | | 2018-01-18 02:27:57 | Delete |
| -u | Filter | | 2018-01-27 04:22:32 | Delete |
| -d | Descriptors | | 2018-02-06 09:57:06 | Delete |
| tt.mol2 | Software | tt.mol2 | 2018-02-06 13:05:15 | Delete |
| -d | Descriptors | | 2018-02-16 01:28:57 | Delete |
| -d | Descriptors | | 2018-03-13 05:30:08 | Delete |
| -d | Descriptors | | 2018-03-16 19:00:40 | Delete |
| -d | Descriptors | | 2018-03-27 03:56:16 | Delete |
| -d | Descriptors | | 2018-03-27 04:10:16 | Delete |
| -u | Filter | | 2018-03-27 04:26:05 | Delete |
| -d | Descriptors | | 2018-04-06 13:50:44 | Delete |
| -d | Descriptors | | 2018-04-18 14:18:50 | Delete |
| -d | Descriptors | | 2018-04-26 12:03:59 | Delete |
| -d | Descriptors | | 2018-06-13 14:59:34 | Delete |
| PDBBind 2017 Rule of 3 | Molecules | This is a subset of PDBBind 2017 containing only protein-fragment complexes. I filtered the PDBBind using the cutoff MW <= 300Da, similar to the Rule of Three for fragments. | 2018-07-09 17:55:46 | Delete |
| -d | Descriptors | | 2018-07-09 18:01:19 | Delete |
| pdbbind300 | Molecules | PDBBind dataset filtered using Rule of 3 | 2018-07-09 18:05:58 | Delete |
| -d | Descriptors | | 2018-07-09 18:06:16 | Delete |
| Extract_fragments | Descriptors | | 2018-07-09 18:06:51 | Delete |
| Molecules | | 2018-07-10 02:10:32 | Delete |
| pdbbind300train | Molecules | PDBBind 2017 protein-fragments dataset. | 2018-07-10 02:29:28 | Delete |
| scoring_rfscore_fragments | SF | | 2018-07-10 02:58:34 | Delete |
| test_train_300_desc | Descriptors | | 2018-07-10 04:17:55 | Delete |
| nooverlap_scoring | SF | | 2018-07-10 04:30:44 | Delete |
| nooverlap_scoring | SF | | 2018-07-10 04:57:10 | Delete |
| -d | Descriptors | | 2018-07-11 20:03:38 | Delete |
| -d | Descriptors | | 2018-07-11 20:06:15 | Delete |
| -d | Descriptors | | 2018-09-08 13:36:56 | Delete |
| testing_marcos | Descriptors | | 2018-10-31 10:20:07 | Delete |
| -d | Descriptors | | 2018-12-14 04:06:38 | Delete |
| -d | Descriptors | | 2018-12-14 04:14:00 | Delete |
| -d | Descriptors | | 2018-12-14 04:17:43 | Delete |
| -d | Descriptors | | 2019-01-04 14:43:02 | Delete |
| -d | Descriptors | | 2019-02-07 11:04:28 | Delete |
| -d | Descriptors | | 2019-07-08 06:05:13 | Delete |
| -d | Descriptors | | 2019-07-14 09:23:22 | Delete |
| -d | Descriptors | | 2019-07-14 09:27:08 | Delete |
| -d | Descriptors | | 2019-07-14 09:29:46 | Delete |
| -d | Descriptors | | 2019-07-16 12:23:30 | Delete |
| -d | Descriptors | | 2019-08-27 07:05:21 | Delete |
| -d | Descriptors | | 2019-10-09 20:06:08 | Delete |
| -d | Descriptors | | 2019-10-22 08:11:06 | Delete |
| Retest_Ecfp | SF | Retest_Ecfp | 2019-12-31 19:52:17 | Delete |
| r3 | Descriptors | r3 | 2020-03-16 06:50:34 | Delete |
| test_ddb_14 | SF | | 2020-03-22 23:24:57 | Delete |
| Lets_test_if_email_is_working | SF | | 2020-03-23 00:05:01 | Delete |
| email_test2 | SF | | 2020-03-23 00:07:59 | Delete |
| test_email2 | SF | | 2020-03-23 01:58:01 | Delete |
| test_email3 | SF | | 2020-03-23 02:17:58 | Delete |
| filter_test | Filter | | 2020-03-23 02:32:01 | Delete |
