Binding Affinity Prediction ML Frameworks

Tools for predicting the strength and specificity of interactions between ligands (drugs, compounds) and protein targets using ML/DL. Includes binding residue identification and kinase bioactivity prediction. Does NOT include general protein-protein interactions, protein structure prediction, or broader drug discovery pipelines.

There are 58 binding affinity prediction frameworks tracked. 4 score above 50 (established tier). The highest-rated is BioinfoMachineLearning/PoseBench at 58/100 with 213 stars and 148 monthly downloads.

Get all 58 projects as JSON

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#	Framework	Score	Tier	Stars	Language
1	BioinfoMachineLearning/PoseBench Comprehensive benchmarking of protein-ligand structure prediction methods....	58	Established	213	Jupyter Notebook
2	pritampanda15/PandaDock PandaDock: Physics based Molecular Docking with GNN Scoring	55	Established	95	Python
3	kexinhuang12345/DeepPurpose A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function...	53	Established	1,134	Jupyter Notebook
4	kamerlinlab/KIF KIF - Key Interactions Finder. A python package to identify the key...	50	Established	34	Python
5	maranasgroup/CatPred Machine Learning models for in vitro enzyme kinetic parameter prediction	48	Emerging	77	Python
6	BioinfoMachineLearning/FlowDock A geometric flow matching model for generative protein-ligand docking and...	41	Emerging	129	Python
7	jamesgleave/DD_protocol Official repository for the Deep Docking protocol	40	Emerging	125	Python
8	lightdock/lightdock Protein-protein, protein-peptide and protein-DNA docking framework based on...	40	Emerging	384	Python
9	Arturossi/OCDocker OCdocker is a docking automation suite with scoring functions consensus based on ML	39	Emerging	3	Python
10	davidkastner/quantumPDB Workflow for generate a database of proteins with quantum properties	38	Emerging	12	Python
11	QizhiPei/FABind FABind: Fast and Accurate Protein-Ligand Binding (NeurIPS 2023)	36	Emerging	140	Python
12	kYangLi/DeepH-dock DeepH-dock seamlessly integrates deep learning with first-principles...	35	Emerging	29	Python
13	XieResearchGroup/eMOSAIC Source code for "Multimodal out-of-distribution individual uncertainty...	35	Emerging	5	Python
14	insitro/kindel KinDEL is a large DNA-encoded library dataset containing two kinase targets...	35	Emerging	28	Python
15	maxischuh/BarlowDTI Accurate prediction of drug–target interactions in drug discovery.	34	Emerging	10	Python
16	BioinfoMachineLearning/MULTICOM_ligand Comprehensive ensembling of protein-ligand structure and affinity prediction...	34	Emerging	8	Jupyter Notebook
17	AlexanderSychev2005/BindingAffinity This project is the implementation of the Deep Learning model to predict the...	34	Emerging	2	Jupyter Notebook
18	ky66/ROBIN An analysis of a new experimentally-derived nucleic acid binding chemical library	33	Emerging	27	Jupyter Notebook
19	jRicciL/ML-ensemble-docking Improving Structure-Based Virtual Screening with Ensemble Docking and...	33	Emerging	28	Jupyter Notebook
20	QizhiPei/SSM-DTA SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity...	31	Emerging	55	Python
21	ribesstefano/PROTAC-Degradation-Predictor Predicting PROTAC protein degradation activity via machine learning.	31	Emerging	15	Jupyter Notebook
22	RMeli/gnina-torch 🔥 PyTorch implementation of GNINA scoring function for molecular docking	31	Emerging	74	Python
23	Bindwell/APPT Affinity Protein-Protein Transformers—State of the art protein-protein...	29	Experimental	106	Python
24	ChatterjeeAyan/AI-Bind Interpretable AI pipeline improving binding predictions for novel protein...	29	Experimental	32	Jupyter Notebook
25	Gumgo91/AutoTarget A Disease-Associated Drug Target Recommendation System using Node...	29	Experimental	5	Jupyter Notebook
26	ml-jku/hyper-dti HyperPCM: Robust task-conditioned modeling of drug-target interactions	28	Experimental	38	Python
27	PaccMann/paccmann_kinase_binding_residues Comparison of active site and full kinase sequences for drug-target affinity...	28	Experimental	37	Python
28	tiejundong/FlexPose FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.	27	Experimental	55	Python
29	a-r-j/CPDB Cython implementation of PDB -> DataFrame parsing	26	Experimental	33	Cython
30	LDeng0205/confidence-bootstrapping Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.	26	Experimental	27	Python
31	jrem-chem/GPCRLigNet Code for an artificial neural net classifier of small molecule GPCR activity	25	Experimental	5	PureBasic
32	kYangLi/DeepH-pack-docs The documentation of DeepH-pack, the latest iteration of DeepH, unites all...	25	Experimental	16	Python
33	SourangshuGhosh/coronavirus_cure_DeepLearning Using deep learning to generate novel molecules as candidates for binding...	25	Experimental	5	Jupyter Notebook
34	ribesstefano/PROTAC-Splitter PROTAC-Splitter is a machine learning framework designed for automated...	24	Experimental	18	Jupyter Notebook
35	Barabasi-Lab/AI-Bind Interpretable AI pipeline improving binding predictions for novel protein...	24	Experimental	41	Jupyter Notebook
36	HySonLab/LINKER LINKER: Learning Interactions Between Functional Groups and Residues With...	23	Experimental	8	Jupyter Notebook
37	lee-jwon/BInD Official repository for BInD (Bond and Interaction generating Diffusion model)	22	Experimental	30	Python
38	jahnl/binding_in_disorder Prediction of Binding Residues in Disordered Regions Based on Protein...	20	Experimental	11	Python
39	Rohit-K814307/cycle_consistent_conditional_protein_generative_adversarial_network Algorithmic code for "Adversarially Driven Generation of De Novo Proteins...	19	Experimental	—	Jupyter Notebook
40	afm719/AntibacterialAI The goal of this project is to apply Deep Learning techniques to generate...	17	Experimental	2	Jupyter Notebook
41	Simran-Sodhi/drug-design-dynamics Protein–ligand interaction prediction using Metropolis simulations and...	15	Experimental	1	Go
42	lan-codes/Benchmark_VS Integrating Machine Learning-Based Pose Sampling with Established Scoring...	15	Experimental	6	Jupyter Notebook
43	wtaisner/chimerax-ligand-recognizer This bundle provides ChimeraX command for recognizing ligands in cryoEM and...	15	Experimental	6	Python
44	jkarolczak/ligand-classification Project examing sparse deep learning architectures for ligand classification.	15	Experimental	10	Jupyter Notebook
45	drbenedictpaul/judock An open-source, AI-powered virtual screening platform for phytocompounds....	14	Experimental	—	Julia
46	sobazino/SAP Drug–target interaction prediction	14	Experimental	3	Python
47	sobazino/TAeGat Drug–target interaction prediction	14	Experimental	3	Python
48	sieber-lab/AIbiotics DL Pipeline for Antibiotic Discovery	14	Experimental	3	Jupyter Notebook
49	manbaritone/SynProtX SynProtX is a deep learning model leveraging large-scale proteomics,...	13	Experimental	2	Jupyter Notebook
50	ORNL/affinity_pred Protein-ligand affinity prediction using NLP	13	Experimental	7	Jupyter Notebook
51	OthmanSALAHI/BindingAffinity predict the strength of the interaction (binding affinity) between a drug...	13	Experimental	—	TypeScript
52	Brendan-P-Moore/BindingAffinity Predicts the dissociation coefficients between drug-protein (target) pairs...	13	Experimental	5	Jupyter Notebook
53	horsepurve/DeepB3P3 Masked peptides for low-data peptide drug discovery (BiB 2023)	12	Experimental	4	Jupyter Notebook
54	IPSProjects/SDR Structure Database Repository	12	Experimental	3	—
55	TangSoftwareLab/KiBA An integrated drug-target bioactivity matrix across 52,498 chemical...	11	Experimental	2	—
56	russelllab/kinaseResistance A method to predict activating, deactivating and resistance mutations in kinases	11	Experimental	2	JavaScript
57	Fraunhofer-ITMP/E3_binder_Model Source code and dataset for paper titled "Pharmacophore-based ML model to...	11	Experimental	2	R
58	M4Marvin/plb_jnu Deep Learning Framework for Protein-Ligand Binding Affinity Prediction	10	Experimental	1	Jupyter Notebook