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 60 binding affinity prediction frameworks tracked. 4 score above 50 (established tier). The highest-rated is pritampanda15/PandaDock at 62/100 with 95 stars.

Get all 60 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=ml-frameworks&subcategory=binding-affinity-prediction&limit=20"

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#	Framework	Score	Tier	Stars	Language
1	pritampanda15/PandaDock PandaDock: Physics based Molecular Docking with GNN Scoring	62	Established	95	Python
2	kexinhuang12345/DeepPurpose A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function...	60	Established	1,134	Jupyter Notebook
3	BioinfoMachineLearning/PoseBench Comprehensive benchmarking of protein-ligand structure prediction methods....	57	Established	213	Jupyter Notebook
4	maranasgroup/CatPred Machine Learning models for in vitro enzyme kinetic parameter prediction	55	Established	77	Python
5	kamerlinlab/KIF KIF - Key Interactions Finder. A python package to identify the key...	49	Emerging	34	Python
6	BioinfoMachineLearning/FlowDock A geometric flow matching model for generative protein-ligand docking and...	48	Emerging	129	Python
7	jamesgleave/DD_protocol Official repository for the Deep Docking protocol	47	Emerging	125	Python
8	lightdock/lightdock Protein-protein, protein-peptide and protein-DNA docking framework based on...	47	Emerging	384	Python
9	davidkastner/quantumPDB Workflow for generate a database of proteins with quantum properties	45	Emerging	12	Python
10	QizhiPei/FABind FABind: Fast and Accurate Protein-Ligand Binding (NeurIPS 2023)	43	Emerging	140	Python
11	insitro/kindel KinDEL is a large DNA-encoded library dataset containing two kinase targets...	42	Emerging	28	Python
12	maxischuh/BarlowDTI Accurate prediction of drug–target interactions in drug discovery.	41	Emerging	10	Python
13	jRicciL/ML-ensemble-docking Improving Structure-Based Virtual Screening with Ensemble Docking and...	40	Emerging	28	Jupyter Notebook
14	ky66/ROBIN An analysis of a new experimentally-derived nucleic acid binding chemical library	40	Emerging	27	Jupyter Notebook
15	QizhiPei/SSM-DTA SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity...	38	Emerging	55	Python
16	ribesstefano/PROTAC-Degradation-Predictor Predicting PROTAC protein degradation activity via machine learning.	38	Emerging	15	Jupyter Notebook
17	AlexanderSychev2005/BindingAffinity This project is the implementation of the Deep Learning model to predict the...	38	Emerging	2	Jupyter Notebook
18	RMeli/gnina-torch 🔥 PyTorch implementation of GNINA scoring function for molecular docking	38	Emerging	74	Python
19	Arturossi/OCDocker OCdocker is a docking automation suite with scoring functions consensus based on ML	38	Emerging	3	Python
20	XieResearchGroup/eMOSAIC Source code for "Multimodal out-of-distribution individual uncertainty...	38	Emerging	5	Python
21	ChatterjeeAyan/AI-Bind Interpretable AI pipeline improving binding predictions for novel protein...	36	Emerging	32	Jupyter Notebook
22	kYangLi/DeepH-dock DeepH-dock seamlessly integrates deep learning with first-principles...	36	Emerging	29	Python
23	Bindwell/APPT Affinity Protein-Protein Transformers—State of the art protein-protein...	36	Emerging	106	Python
24	BioinfoMachineLearning/MULTICOM_ligand Comprehensive ensembling of protein-ligand structure and affinity prediction...	35	Emerging	8	Jupyter Notebook
25	ml-jku/hyper-dti HyperPCM: Robust task-conditioned modeling of drug-target interactions	35	Emerging	38	Python
26	PaccMann/paccmann_kinase_binding_residues Comparison of active site and full kinase sequences for drug-target affinity...	35	Emerging	37	Python
27	tiejundong/FlexPose FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.	34	Emerging	55	Python
28	LDeng0205/confidence-bootstrapping Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.	33	Emerging	27	Python
29	Gumgo91/AutoTarget A Disease-Associated Drug Target Recommendation System using Node...	33	Emerging	5	Jupyter Notebook
30	a-r-j/CPDB Cython implementation of PDB -> DataFrame parsing	33	Emerging	33	Cython
31	jrem-chem/GPCRLigNet Code for an artificial neural net classifier of small molecule GPCR activity	32	Emerging	5	PureBasic
32	SourangshuGhosh/coronavirus_cure_DeepLearning Using deep learning to generate novel molecules as candidates for binding...	32	Emerging	5	Jupyter Notebook
33	ribesstefano/PROTAC-Splitter PROTAC-Splitter is a machine learning framework designed for automated...	31	Emerging	18	Jupyter Notebook
34	Barabasi-Lab/AI-Bind Interpretable AI pipeline improving binding predictions for novel protein...	31	Emerging	41	Jupyter Notebook
35	lee-jwon/BInD Official repository for BInD (Bond and Interaction generating Diffusion model)	29	Experimental	30	Python
36	kYangLi/DeepH-pack-docs The documentation of DeepH-pack, the latest iteration of DeepH, unites all...	29	Experimental	16	Python
37	jahnl/binding_in_disorder Prediction of Binding Residues in Disordered Regions Based on Protein...	27	Experimental	11	Python
38	HySonLab/LINKER LINKER: Learning Interactions Between Functional Groups and Residues With...	27	Experimental	8	Jupyter Notebook
39	afm719/AntibacterialAI The goal of this project is to apply Deep Learning techniques to generate...	23	Experimental	2	Jupyter Notebook
40	Simran-Sodhi/drug-design-dynamics Protein–ligand interaction prediction using Metropolis simulations and...	22	Experimental	1	Go
41	lan-codes/Benchmark_VS Integrating Machine Learning-Based Pose Sampling with Established Scoring...	22	Experimental	6	Jupyter Notebook
42	wtaisner/chimerax-ligand-recognizer This bundle provides ChimeraX command for recognizing ligands in cryoEM and...	22	Experimental	6	Python
43	jkarolczak/ligand-classification Project examing sparse deep learning architectures for ligand classification.	22	Experimental	10	Jupyter Notebook
44	sieber-lab/AIbiotics DL Pipeline for Antibiotic Discovery	21	Experimental	3	Jupyter Notebook
45	manbaritone/SynProtX SynProtX is a deep learning model leveraging large-scale proteomics,...	20	Experimental	2	Jupyter Notebook
46	Brendan-P-Moore/BindingAffinity Predicts the dissociation coefficients between drug-protein (target) pairs...	20	Experimental	5	Jupyter Notebook
47	sobazino/TAeGat Drug–target interaction prediction	20	Experimental	3	Python
48	sobazino/SAP Drug–target interaction prediction	20	Experimental	3	Python
49	ORNL/affinity_pred Protein-ligand affinity prediction using NLP	20	Experimental	7	Jupyter Notebook
50	IPSProjects/SDR Structure Database Repository	19	Experimental	3	—
51	horsepurve/DeepB3P3 Masked peptides for low-data peptide drug discovery (BiB 2023)	19	Experimental	4	Jupyter Notebook
52	russelllab/kinaseResistance A method to predict activating, deactivating and resistance mutations in kinases	18	Experimental	2	JavaScript
53	TangSoftwareLab/KiBA An integrated drug-target bioactivity matrix across 52,498 chemical...	18	Experimental	2	—
54	Fraunhofer-ITMP/E3_binder_Model Source code and dataset for paper titled "Pharmacophore-based ML model to...	18	Experimental	2	R
55	M4Marvin/plb_jnu Deep Learning Framework for Protein-Ligand Binding Affinity Prediction	17	Experimental	1	Jupyter Notebook
56	OthmanSALAHI/BindingAffinity predict the strength of the interaction (binding affinity) between a drug...	15	Experimental	—	TypeScript
57	drbenedictpaul/judock An open-source, AI-powered virtual screening platform for phytocompounds....	14	Experimental	—	Julia
58	ytabatabaee/DL4H Final Project of Deep Learning for Healthcare Spring 2022 - Reproducing DeepDTA	12	Experimental	5	Jupyter Notebook
59	Psygoal/Deep-Identification-of-Key-Intermediates-DIKI Deep Identification of Key Intermediates	12	Experimental	6	Python
60	SYNBI-KAIST/HJ-DTA-DataBias BASE: a web service for providing compound-protein binding affinity...	11	Experimental	—	Jupyter Notebook