Drug Discovery

Drug discovery is the task of applying machine learning to discover new candidate drugs.

( Image credit: A Turing Test for Molecular Generators )

Papers

Recently Added Most Hyped Most Active Needs Verification Most Verified

Showing 1–50 of 1337 papers

Title	Date	Tasks	Status	Hype	Score
TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery	Feb 16, 2022	BIG-bench Machine LearningDrug Discovery	CodeCode Available	3	5
FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction	Dec 14, 2024	Blind DockingDrug Discovery	CodeCode Available	3	5
Uni-QSAR: an Auto-ML Tool for Molecular Property Prediction	Apr 24, 2023	Drug DiscoveryModel Selection	CodeCode Available	3	5
Robust deep learning based protein sequence design using ProteinMPNN	Jun 4, 2022	Deep LearningDrug Discovery	CodeCode Available	3	5
ACEGEN: Reinforcement learning of generative chemical agents for drug discovery	May 7, 2024	BenchmarkingDecision Making	CodeCode Available	3	5
Test-Time Training Scaling Laws for Chemical Exploration in Drug Design	Jan 31, 2025	Drug DesignDrug Discovery	CodeCode Available	3	5
REvoLd: Ultra-Large Library Screening with an Evolutionary Algorithm in Rosetta	Apr 26, 2024	Drug Discovery	CodeCode Available	3	5
Deep Learning for Protein-Ligand Docking: Are We There Yet?	May 23, 2024	Deep LearningDrug Discovery	CodeCode Available	3	5
Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity	Mar 30, 2017	Drug DiscoveryMolecular Docking	CodeCode Available	3	5
A Python library for efficient computation of molecular fingerprints	Mar 27, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	3	5
^2DFT: A Universal Quantum Chemistry Dataset of Drug-Like Molecules and a Benchmark for Neural Network Potentials	Jun 20, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	3	5
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation	Feb 18, 2025	3D Generation3D Molecule Generation	CodeCode Available	2	5
PPFlow: Target-aware Peptide Design with Torsional Flow Matching	Mar 5, 2024	Drug DesignDrug Discovery	CodeCode Available	2	5
PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning	Jun 24, 2025	BenchmarkingDrug Discovery	CodeCode Available	2	5
Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry	Jan 7, 2024	Data AugmentationDrug Discovery	CodeCode Available	2	5
ChemCrow: Augmenting large-language models with chemistry tools	Apr 11, 2023	Computational chemistryDrug Discovery	CodeCode Available	2	5
Large AI Models in Health Informatics: Applications, Challenges, and the Future	Mar 21, 2023	Decision MakingDrug Discovery	CodeCode Available	2	5
LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset	Feb 14, 2024	Drug Discovery	CodeCode Available	2	5
Generative Flows on Synthetic Pathway for Drug Design	Oct 6, 2024	Drug DesignDrug Discovery	CodeCode Available	2	5
Learning Causally Invariant Representations for Out-of-Distribution Generalization on Graphs	Feb 11, 2022	Drug DiscoveryGraph Learning	CodeCode Available	2	5
FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation	Mar 29, 2024	Blind DockingDrug Discovery	CodeCode Available	2	5
Accelerating Material Design with the Generative Toolkit for Scientific Discovery	Jul 8, 2022	Drug DiscoveryMaterials Screening	CodeCode Available	2	5
JAX, M.D.: A Framework for Differentiable Physics	Dec 9, 2019	Drug DiscoveryGPU	CodeCode Available	2	5
ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation	Oct 29, 2024	Drug Discovery	CodeCode Available	2	5
Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology	Apr 16, 2024	Drug DiscoverySelf-Supervised Learning	CodeCode Available	2	5
Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing	Dec 21, 2022	Contrastive LearningDrug Design	CodeCode Available	2	5
ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoning	Jan 11, 2025	Drug Discovery	CodeCode Available	2	5
NeuralPLexer3: Accurate Biomolecular Complex Structure Prediction with Flow Models	Dec 14, 2024	BenchmarkingDrug Design	CodeCode Available	2	5
PLAPT: Protein-Ligand Binding Affinity Prediction Using Pretrained Transformers	Feb 8, 2024	Drug DiscoveryPrediction	CodeCode Available	2	5
A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications	Feb 16, 2022	Drug DiscoveryGraph Representation Learning	CodeCode Available	2	5
Full-Atom Peptide Design based on Multi-modal Flow Matching	Jun 2, 2024	Drug Discovery	CodeCode Available	2	5
Graph Diffusion Transformers for Multi-Conditional Molecular Generation	Jan 24, 2024	DecoderDenoising	CodeCode Available	2	5
DistMLIP: A Distributed Inference Platform for Machine Learning Interatomic Potentials	May 28, 2025	Drug Discoverygraph partitioning	CodeCode Available	2	5
DeepPurpose: a Deep Learning Library for Drug-Target Interaction Prediction	Apr 19, 2020	Deep LearningDrug Discovery	CodeCode Available	2	5
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding	Nov 21, 2022	Drug Discovery	CodeCode Available	2	5
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction	Feb 7, 2022	Blind DockingDeep Learning	CodeCode Available	2	5
DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models	Apr 8, 2023	Drug DiscoveryProtein Design	CodeCode Available	2	5
Diffusion Models for Molecules: A Survey of Methods and Tasks	Feb 13, 2025	DiversityDrug Discovery	CodeCode Available	2	5
Equivariant Energy-Guided SDE for Inverse Molecular Design	Sep 30, 2022	3D Molecule GenerationDrug Discovery	CodeCode Available	2	5
Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond	Jul 13, 2023	Drug DesignDrug Discovery	CodeCode Available	2	5
Data-Driven Parametrization of Molecular Mechanics Force Fields for Expansive Chemical Space Coverage	Aug 23, 2024	Computational EfficiencyDrug Discovery	CodeCode Available	2	5
Fast and Accurate Blind Flexible Docking	Feb 20, 2025	Blind DockingComputational Efficiency	CodeCode Available	2	5
Generating 3D Molecules for Target Protein Binding	Apr 19, 2022	Drug DiscoveryGraph Neural Network	CodeCode Available	2	5
Generative Artificial Intelligence for Navigating Synthesizable Chemical Space	Oct 4, 2024	Drug DiscoveryNavigate	CodeCode Available	2	5
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation	Mar 6, 2022	Drug Discovery	CodeCode Available	2	5
GFT: Graph Foundation Model with Transferable Tree Vocabulary	Nov 9, 2024	Drug DiscoveryGraph Learning	CodeCode Available	2	5
Concept Bottleneck Language Models For protein design	Nov 9, 2024	Decision MakingDrug Discovery	CodeCode Available	2	5
DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design	Feb 26, 2024	AvgDrug Design	CodeCode Available	2	5
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning	Feb 27, 2024	Drug DiscoveryForward reaction prediction	CodeCode Available	2	5
Multi-Objective Molecule Generation using Interpretable Substructures	Feb 8, 2020	DiversityDrug Design	CodeCode Available	2	5

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All datasets QM9 Tox21 BACE HIV dataset MUV ToxCast BBBP BindingDB clintox DAVIS-DTA KIBA LIT-PCBA(ALDH1)

Benchmark Results

#	Model	Metric	Claimed	Verified	Status
1	Molecular Graph Convolutions	Error ratio	2.59	—	Unverified
2	Gated Graph Sequence NN	Error ratio	1.36	—	Unverified
3	MPNNs	Error ratio	0.68	—	Unverified
4	DeepMoleNet	Error ratio	0.53	—	Unverified
5	DimeNet	Error ratio	0.44	—	Unverified
6	PaiNN	Error ratio	0.41	—	Unverified
7	DimeNet++	Error ratio	0.41	—	Unverified
8	ComENet	Error ratio	0.4	—	Unverified
9	SphereNet	Error ratio	0.39	—	Unverified
10	MXMNet	Error ratio	0.38	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	elEmBERT-V1	AUC	0.96	—	Unverified
2	TrimNet + Perforated Backpropagation	AUC	0.89	—	Unverified
3	SSVAE with multiple SMILES	AUC	0.87	—	Unverified
4	Ensemble predictor	AUC	0.86	—	Unverified
5	TrimNet	AUC	0.86	—	Unverified
6	GraphConv + dummy super node	AUC	0.85	—	Unverified
7	GraphConv	AUC	0.85	—	Unverified
8	SNN (SELU Network)	AUC	0.85	—	Unverified
9	ContextPred	AUC	0.78	—	Unverified
10	GIT-Mol(G+S)	AUC	0.76	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	TrimNet	AUC	0.88	—	Unverified
2	Ensemble locally constant network	AUC	0.87	—	Unverified
3	ProtoW-L2	AUC	0.87	—	Unverified
4	elEmBERT-V1	AUC	0.86	—	Unverified
5	ContextPred	AUC	0.85	—	Unverified
6	GIT-Mol(G+S)	AUC	0.81	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GraphConv + dummy super node + focal loss	AUC	0.85	—	Unverified
2	GraphConv	AUC	0.82	—	Unverified
3	TrimNet	AUC	0.8	—	Unverified
4	ContextPred	AUC	0.8	—	Unverified
5	RNN-DFS	AUC	0.63	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	TrimNet	AUC	0.85	—	Unverified
2	GraphConv + dummy super node	AUC	0.85	—	Unverified
3	GraphConv	AUC	0.84	—	Unverified
4	ContextPred	AUC	0.81	—	Unverified
5	RNN-DFS	AUC	0.65	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	TrimNet	AUC	0.78	—	Unverified
2	GraphConv + dummy super node	AUC	0.77	—	Unverified
3	GraphConv	AUC	0.75	—	Unverified
4	GIT-Mol(G+S)	AUC	0.67	—	Unverified
5	ContextPred	AUC	0.66	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	ProtoW-L2	AUC	0.92	—	Unverified
2	elEmBERT-V1	AUC	0.91	—	Unverified
3	GIT-Mol(G+S)	AUC	0.74	—	Unverified
4	ContextPred	AUC	0.69	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	AttentionSiteDTI	AUC	0.97	—	Unverified
2	GLAM	AUC	0.95	—	Unverified
3	TransformerCPI	AUC	0.94	—	Unverified
4	DGraphDTA	AUC	0.92	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	BiLSTM	AUC	0.97	—	Unverified
2	TrimNet	AUC	0.95	—	Unverified
3	GIT-Mol(G+S)	AUC	0.88	—	Unverified
4	ContextPred	AUC	0.73	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	SMT-DTA	CI	0.89	—	Unverified
2	DeepPurpose	CI	0.88	—	Unverified
3	DeepDTA	CI	0.87	—	Unverified
4	GraphDTA	CI	0.86	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	SMT-DTA	CI	0.89	—	Unverified
2	DeepPurpose	CI	0.87	—	Unverified
3	DeepDTA	CI	0.86	—	Unverified
4	GraphDTA	CI	0.86	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	EGT+TGT-At-DP	AUC	0.81	—	Unverified
2	GLAM	AUC	0.76	—	Unverified
3	TransformerCPI	AUC	0.69	—	Unverified
4	DGraphDTA	AUC	0.68	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	EGT+TGT-At-DP	AUC	0.75	—	Unverified
2	GLAM	AUC	0.71	—	Unverified
3	TransformerCPI	AUC	0.65	—	Unverified
4	DGraphDTA	AUC	0.63	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	EGT+TGT-At-DP	AUC	0.74	—	Unverified
2	GLAM	AUC	0.73	—	Unverified
3	TransformerCPI	AUC	0.68	—	Unverified
4	DGraphDTA	AUC	0.67	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	elEmBERT-V1	AUC	0.78	—	Unverified
2	Ensemble locally constant networks	AUC	0.69	—	Unverified
3	GIT-Mol(G+S)	AUC	0.63	—	Unverified
4	ContextPred	AUC	0.63	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	AUC	0.67	—	Unverified
2	TransformerCPI	AUC	0.62	—	Unverified
3	DGraphDTA	AUC	0.61	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	DeepDTA	Pearson Correlation	0.85	—	Unverified
2	DeepAffinity	Pearson Correlation	0.84	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GraphConv + dummy super node	AUC	0.87	—	Unverified
2	GraphConv	AUC	0.86	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	AUC	0.89	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	AUC	0.93	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	HierG2G	Diversity	0.19	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Multi-input Neural network with Attention	AUC	0.91	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	RMSE	0.59	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	RMSE	1.32	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	RMSE	0.6	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Ensemble locally constant networks	RMSE	1.22	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	HierG2G	Diversity	0.48	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	AUC	0.74	—	Unverified