Molecular Structure Prediction ML Frameworks

Tools and resources for predicting molecular structures, properties, and interactions using ML—including small-molecule drug discovery, protein folding, molecular docking, and structural bioinformatics. Does NOT include general sequence design, peptide property prediction, or non-structural bioinformatics tasks.

There are 30 molecular structure prediction frameworks tracked. 1 score above 50 (established tier). The highest-rated is josiehong/awesome-smallmol-massspec-ml at 50/100 with 36 stars.

Get all 30 projects as JSON

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

Open to everyone — 100 requests/day, no key needed. Get a free key for 1,000/day.

#	Framework	Score	Tier	Stars	Language
1	josiehong/awesome-smallmol-massspec-ml Awesome papers and codes list of small molecule mass spectrometry-related...	50	Established	36	—
2	GoekeLab/awesome-nanopore A curated list of awesome nanopore analysis tools.	49	Emerging	307	—
3	kjappelbaum/awesome-chemistry-datasets overview of datasets for ML in chemistry	49	Emerging	394	—
4	inoue0426/awesome-computational-biology Awesome list of computational biology.	46	Emerging	120	Python
5	HongxinXiang/awesome-ai-bioinformatics A curated list of awesome AI and Bioinformatics.	42	Emerging	51	—
6	benb111/awesome-small-molecule-ml A curated list of resources for machine learning for small-molecule drug discovery	42	Emerging	238	—
7	gozsari/Awesome-GNN-based-drug-discovery This is a curated list of research papers, resources and tools related to...	40	Emerging	62	—
8	LiuGaoyong/AwesomeMLP Awesome Machine Learning Interatomic Potentials	39	Emerging	11	—
9	opendilab/awesome-AI-based-protein-design A collection of research papers for AI-based protein design	38	Emerging	295	—
10	sherrylixuecheng/awesome-ai4chem Awesome AI for chemistry papers	37	Emerging	46	—
11	MaybeBio/Awesome-IDR-Prediction Curated Labs, Tools for Protein Intrinsic Disorder (IDR) prediction.	35	Emerging	5	—
12	Thinklab-SJTU/awesome-molecular-docking We would like to maintain a list of resources which aim to solve molecular...	34	Emerging	106	—
13	Ahhmedsamehh/Bioinformatics_resources This repo is dedicated to make bioinformatics resources available for anyone...	32	Emerging	28	—
14	asarigun/awesome-denovo-papers Awesome De novo drugs design papers	32	Emerging	92	—
15	twoXes/awesome-structural-bioinformatics Structural Bioinformatics is awesome. Throw your textbook in the garbage,...	31	Emerging	76	Python
16	Grenzlinie/awesome-ai4ms-paper-and-websites This repository is a collection of my thoughts, summaries, and reflections...	29	Experimental	7	—
17	chenxingqiang/Awesome_AI_Aided_Drug_Design_Papers https://chenxingqiang.github.io/Awesome_AI_Aided_Drug_Design_Papers/...	29	Experimental	8	—
18	m2d2-labs/awesome-ml-for-biochemistry Community-curated resources for research at the intersection of AI and...	27	Experimental	18	—
19	ngmsonn/Awesome_Network_Pharmacology Awesome Network Pharmacology	25	Experimental	7	—
20	Aavache/awesome-genetic-ai-papers Recent awesome AI papers about genomics.	24	Experimental	3	—
21	Davidlequnchen/Awesome-AM-process-monitoring-control A curated collection of research papers with open-source...	23	Experimental	14	—
22	MOB-sys/awesome-drug-interactions A curated list of drug interaction databases, APIs, tools, and research resources	22	Experimental	—	—
23	wvdon/Awesome-Protein-Design This repository contains a collection of resources and papers on Protein Design.	20	Experimental	7	—
24	cafferychen777/awesome-scrna-annotation A curated list of tools and methods for scRNA-seq cell type annotation	19	Experimental	2	—
25	jvanheld/intro-bioinfo-L2-SV-AMU-SSV3U15_public Cours d'introduction à la bioinformatique, 2ème licence en Sciences de la...	19	Experimental	—	HTML
26	pengzhangzhi/Awesome-Computational-Structural-Biology A curated list of awesome self-learning materials in Computational...	16	Experimental	55	—
27	ngmsonn/Awesome_Drug_Discovery_ML A curated list of awesome lists on Machine Learning for Drug Discovery	13	Experimental	10	—
28	pharmacist-sabot/awesome-warfarin A curated list of awesome open-source projects, research, and resources for...	13	Experimental	—	—
29	poloarol/awesome-computational-biochemistry Papers and Tools that would guide your journey in Computational Biochemistry	11	Experimental	4	—
30	Jiadong001/AI4Bio_Paper_Reading_List List of latest/classical papers about AI for Biology. Beginning in 2023....	11	Experimental	3	—

Comparisons in this category

awesome-smallmol-massspec-ml and awesome-small-molecule-ml (50 vs 42) awesome-small-molecule-ml and awesome-ml-for-biochemistry (42 vs 27) awesome-ai-bioinformatics and awesome-ml-for-biochemistry (42 vs 27)