Omkar2118/datasets huggingface dataset:
BindingDB
Full name: The Binding Database

BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. As of May 27, 2022, BindingDB contains 41,296 Entries, each with a DOI, containing 2,519,702 binding data for 8,810 protein targets and 1,080,101 small molecules. There are 5,988 protein-ligand crystal structures with BindingDB affinity measurements for proteins with 100% sequence identity, and 11,442 crystal structures allowing proteins to 85% sequence identity.You can also use BindingDB data through the Registry of Open Data on AWS: https://registry.opendata.aws/binding-db. This dataset using the split by TransformerCPI(doi.org/10.1093/bioinformatics/btaa524)
LIT-PCBA(ALDH1)
Full name: ALDH1 target of LIT-PCBA Dataset

Comparative evaluation of virtual screening methods requires a rigorous benchmarking procedure on diverse, realistic, and unbiased data sets. Recent investigations from numerous research groups unambiguously demonstrate that artificially constructed ligand sets classically used by the community (e.g., DUD, DUD-E, MUV) are unfortunately biased by both obvious and hidden chemical biases, therefore overestimating the true accuracy of virtual screening methods. We herewith present a novel data set (LIT-PCBA) specifically designed for virtual screening and machine learning. LIT-PCBA relies on 149 dose–response PubChem bioassays that were additionally processed to remove false positives and assay artifacts and keep active and inactive compounds within similar molecular property ranges. To ascertain that the data set is suited to both ligand-based and structure-based virtual screening, target sets were restricted to single protein targets for which at least one X-ray structure is available in complex with ligands of the same phenotype (e.g., inhibitor, inverse agonist) as that of the PubChem active compounds. Preliminary virtual screening on the 21 remaining target sets with state-of-the-art orthogonal methods (2D fingerprint similarity, 3D shape similarity, molecular docking) enabled us to select 15 target sets for which at least one of the three screening methods is able to enrich the top 1%-ranked compounds in true actives by at least a factor of 2. The corresponding ligand sets (training, validation) were finally unbiased by the recently described asymmetric validation embedding (AVE) procedure to afford the LIT-PCBA data set, consisting of 15 targets and 7844 confirmed active and 407,381 confirmed inactive compounds. The data set mimics experimental screening decks in terms of hit rate (ratio of active to inactive compounds) and potency distribution. It is available online at http://drugdesign.unistra.fr/LIT-PCBA for download and for benchmarking novel virtual screening methods, notably those relying on machine learning.

Introducing paper: An adaptive graph learning method for automated molecular interactions and properties predictions
LIT-PCBA(ESR1_ant)
Full name: ESR1_ant target of LIT-PCBA Dataset

Comparative evaluation of virtual screening methods requires a rigorous benchmarking procedure on diverse, realistic, and unbiased data sets. Recent investigations from numerous research groups unambiguously demonstrate that artificially constructed ligand sets classically used by the community (e.g., DUD, DUD-E, MUV) are unfortunately biased by both obvious and hidden chemical biases, therefore overestimating the true accuracy of virtual screening methods. We herewith present a novel data set (LIT-PCBA) specifically designed for virtual screening and machine learning. LIT-PCBA relies on 149 dose–response PubChem bioassays that were additionally processed to remove false positives and assay artifacts and keep active and inactive compounds within similar molecular property ranges. To ascertain that the data set is suited to both ligand-based and structure-based virtual screening, target sets were restricted to single protein targets for which at least one X-ray structure is available in complex with ligands of the same phenotype (e.g., inhibitor, inverse agonist) as that of the PubChem active compounds. Preliminary virtual screening on the 21 remaining target sets with state-of-the-art orthogonal methods (2D fingerprint similarity, 3D shape similarity, molecular docking) enabled us to select 15 target sets for which at least one of the three screening methods is able to enrich the top 1%-ranked compounds in true actives by at least a factor of 2. The corresponding ligand sets (training, validation) were finally unbiased by the recently described asymmetric validation embedding (AVE) procedure to afford the LIT-PCBA data set, consisting of 15 targets and 7844 confirmed active and 407,381 confirmed inactive compounds. The data set mimics experimental screening decks in terms of hit rate (ratio of active to inactive compounds) and potency distribution. It is available online at http://drugdesign.unistra.fr/LIT-PCBA for download and for benchmarking novel virtual screening methods, notably those relying on machine learning.

Introducing paper: An adaptive graph learning method for automated molecular interactions and properties predictions
LIT-PCBA(KAT2A)
Full name: KAT2A target of LIT-PCBA Dataset

Comparative evaluation of virtual screening methods requires a rigorous benchmarking procedure on diverse, realistic, and unbiased data sets. Recent investigations from numerous research groups unambiguously demonstrate that artificially constructed ligand sets classically used by the community (e.g., DUD, DUD-E, MUV) are unfortunately biased by both obvious and hidden chemical biases, therefore overestimating the true accuracy of virtual screening methods. We herewith present a novel data set (LIT-PCBA) specifically designed for virtual screening and machine learning. LIT-PCBA relies on 149 dose–response PubChem bioassays that were additionally processed to remove false positives and assay artifacts and keep active and inactive compounds within similar molecular property ranges. To ascertain that the data set is suited to both ligand-based and structure-based virtual screening, target sets were restricted to single protein targets for which at least one X-ray structure is available in complex with ligands of the same phenotype (e.g., inhibitor, inverse agonist) as that of the PubChem active compounds. Preliminary virtual screening on the 21 remaining target sets with state-of-the-art orthogonal methods (2D fingerprint similarity, 3D shape similarity, molecular docking) enabled us to select 15 target sets for which at least one of the three screening methods is able to enrich the top 1%-ranked compounds in true actives by at least a factor of 2. The corresponding ligand sets (training, validation) were finally unbiased by the recently described asymmetric validation embedding (AVE) procedure to afford the LIT-PCBA data set, consisting of 15 targets and 7844 confirmed active and 407,381 confirmed inactive compounds. The data set mimics experimental screening decks in terms of hit rate (ratio of active to inactive compounds) and potency distribution. It is available online at http://drugdesign.unistra.fr/LIT-PCBA for download and for benchmarking novel virtual screening methods, notably those relying on machine learning.
LIT-PCBA(MAPK1)
Full name: MAPK1 target of LIT-PCBA Dataset

Comparative evaluation of virtual screening methods requires a rigorous benchmarking procedure on diverse, realistic, and unbiased data sets. Recent investigations from numerous research groups unambiguously demonstrate that artificially constructed ligand sets classically used by the community (e.g., DUD, DUD-E, MUV) are unfortunately biased by both obvious and hidden chemical biases, therefore overestimating the true accuracy of virtual screening methods. We herewith present a novel data set (LIT-PCBA) specifically designed for virtual screening and machine learning. LIT-PCBA relies on 149 dose–response PubChem bioassays that were additionally processed to remove false positives and assay artifacts and keep active and inactive compounds within similar molecular property ranges. To ascertain that the data set is suited to both ligand-based and structure-based virtual screening, target sets were restricted to single protein targets for which at least one X-ray structure is available in complex with ligands of the same phenotype (e.g., inhibitor, inverse agonist) as that of the PubChem active compounds. Preliminary virtual screening on the 21 remaining target sets with state-of-the-art orthogonal methods (2D fingerprint similarity, 3D shape similarity, molecular docking) enabled us to select 15 target sets for which at least one of the three screening methods is able to enrich the top 1%-ranked compounds in true actives by at least a factor of 2. The corresponding ligand sets (training, validation) were finally unbiased by the recently described asymmetric validation embedding (AVE) procedure to afford the LIT-PCBA data set, consisting of 15 targets and 7844 confirmed active and 407,381 confirmed inactive compounds. The data set mimics experimental screening decks in terms of hit rate (ratio of active to inactive compounds) and potency distribution. It is available online at http://drugdesign.unistra.fr/LIT-PCBA for download and for benchmarking novel virtual screening methods, notably those relying on machine learning.

Introducing paper: An adaptive graph learning method for automated molecular interactions and properties predictions
ESOL (Estimated SOLubility)

ESOL is a water solubility prediction dataset consisting of 1128 samples.

Introducing paper: An adaptive graph learning method for automated molecular interactions and properties predictions
Lipophilicity (logd74)

The lipophilicity database refers to a collection of information related to the lipophilic properties of various molecules. Lipophilicity, also known as hydrophobicity, is a measure of how readily a substance dissolves in nonpolar solvents (such as oil) compared to polar solvents (such as water). In the context of drug discovery and pharmacology, understanding the lipophilicity of compounds is crucial because it affects their absorption, distribution, metabolism, and excretion (ADME) within the body.
FreeSolv (Free Solvation)

The FreeSolv database offers a curated collection of experimental and calculated hydration-free energies for small molecules in water. It includes both experimental values obtained from prior literature and calculated values based on simulations. The goal is to provide accurate hydration-free energy data, which is essential for understanding solvation properties and interactions of molecules in aqueous environments.
BACE (β-secretase enzyme)

The BACE dataset focuses on inhibitors of human beta-secretase 1 (BACE-1).
It includes both quantitative (IC50 values) and qualitative (binary labels) binding results. The dataset comprises small molecule inhibitors across a wide range of affinities, spanning three orders of magnitude (from nanomolar to micromolar IC50 values).
Specifically, it provides:
154 BACE inhibitors for affinity prediction.
20 BACE inhibitors for pose prediction.
34 BACE inhibitors for free energy prediction.
BBBP (Blood-Brain Barrier Penetration)

The BBBP dataset comes from a study focused on modeling and predicting the permeability of the blood-brain barrier. The BBBP dataset contains binary labels indicating whether a compound can penetrate the blood-brain barrier (BBB) or not. Researchers use this dataset to develop and evaluate machine learning methods for predicting BBB permeability. It’s a critical task because understanding which compounds can cross the BBB is essential for drug discovery and designing therapeutics for neurological conditions.

Check https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8708321/
Papyrus

Papyrus is comprised of around 60 million data points. This dataset contains multiple large publicly available datasets such as ChEMBL and ExCAPE-DB combined with several smaller datasets containing high-quality data. The aggregated data has been standardized and normalised in a manner that is suitable for machine learning.

Check https://jcheminf.biomedcentral.com/articles/10.1186/s13321-022-00672-x
SolProp

The SolProp dataset is a valuable resource for predicting the solubility limits of organic solutes in various solvents and at different temperatures. It estimates the solubility of neutral organic molecules in both water and organic solvents across a wide temperature range. The model considers solvation-free energy, solvation enthalpy, Abraham solute parameters, and aqueous solubility at 298K.

Check https://chemrxiv.org/engage/chemrxiv/article-details/6221d767011b586e38bcb0db
ToxCast (Toxicity Forecaster)

ToxCast is an initiative by the U.S. Environmental Protection Agency (EPA) aimed at predicting the potential toxicity of various chemical compounds. It involves high-throughput screening assays that evaluate thousands of chemicals across multiple biological endpoints. These endpoints cover a wide range of effects, including cell cycle disruptions, interactions with steroid receptors, and cytotoxicity.
VizNet-Sato

VizNet-Sato is a dataset from the authors of Sato and is based on the VizNet dataset. The authors choose from VizNet only relational web tables with headers matching their selected 78 DBpedia semantic types.  The selected tables are divided into two categories: Full tables and Multi-column only tables. The first category corresponds to 78,733 selected tables from VizNet, while the second category includes 32,265 tables which have more than one column.  The tables of both categories are divided into 5 subsets to be able to conduct 5-fold cross validation: 4 subsets are used for training and the last for evaluation.

The headers of the columns act as semantic annotations for the Column Type Annotation (CTA) task. Some statistics about both categories of tables are provided in the table below, where "Columns" refers to the number of annotated columns and "Classes" to the number of unique DBpedia semantic types used for annotation.

|                 | Columns | Classes |
|-----------------|---------|---------|
| Full | 120,609 | 78  |
| Multi-column | 74,141 | 78 |

Introducing paper: Sato: Contextual Semantic Type Detection in Tables
Road Anomaly

This dataset contains images of unusual dangers which can be encountered by a vehicle on the road – animals, rocks, traffic cones and other obstacles. Its purpose is testing autonomous driving perception algorithms in rare but safety-critical circumstances.

Introducing paper: Detecting the Unexpected via Image Resynthesis
BBC News Summary

This dataset was created using a dataset used for data categorization that onsists of 2225 documents from the BBC news website corresponding to stories in five topical areas from 2004-2005 used in the paper of D. Greene and P. Cunningham. "Practical Solutions to the Problem of Diagonal Dominance in Kernel Document Clustering", Proc. ICML 2006; whose all rights, including copyright, in the content of the original articles are owned by the BBC. More at http://mlg.ucd.ie/datasets/bbc.html

Introducing paper: Automated News Summarization Using Transformers