De Novo Design Tools

Date	Name	Title	Target	Code
7-Feb-22	LiGAN	Generating 3D molecules conditional on receptor binding sites with deep generative models	Small molecules	Link
15-May-22	Pocket2Mol	Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets	Small molecules	Link
15-Sep-22	ProteinMPNN	Robust deep learning based protein sequence design using ProteinMPNN	Protein design	Link
7-Oct-22	AlphaDrug	AlphaDrug: protein target specific de novo molecular generation	Small molecules	Link
5-Feb-23	FrameDiff	SE(3) diffusion model with application to protein backbone generation	Protein design	Link
11-Jul-23	RFDiffudion	De novo design of protein structure and function with RFdiffusion	Protein design	Link
14-Aug-23	DiffHopp	DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping	Small molecules	Link
7-Sep-23	ResGen	ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling	Small molecules	Link
22-Sep-23	LinkerNet	LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion	Fragments linking	Link
1-Dec-23	KGDiff	KGDiff: towards explainable target-aware molecule generation with knowledge guidance	Small molecules	Link
15-Jan-24	Lingo3DMol	Generation of 3D molecules in pockets via a language model	Small molecules	Link
24-Jan-24	DiffDec	DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model	Small molecules	Link
5-Feb-24	Foldingdiff	Protein structure generation via folding diffusion	Protein design	Link
11-Mar-24	PocketFlow	PocketFlow is a data-and-knowledge-driven structure-based molecular generative model	Small molecules	Link
22-Mar-24	SyntheMol	Generative AI for designing and validating easily synthesizable and structurally novel antibiotics	Small molecules	Link
26-Mar-24	PMDM	A dual diffusion model enables 3D molecule generation and lead optimization based on target pockets	Small molecules	Link
27-Mar-24	DeepICL	3D molecular generative framework for interaction-guided drug design	Small molecules	Link
11-Apr-24	DiffLinker	Equivariant 3D-conditional diffusion model for molecular linker design	Fragments linking	Link
22-Apr-24	dragonfly_gen	Prospective de novo drug design with deep interactome learning	Small molecules	Link
30-Apr-24	ChemoDOTS	ChemoDOTS: a web server to design chemistry-driven focused libraries	Small molecules	Link
2-May-24	SynFlowNet	SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints	Small molecules	Link
3-Jul-24	GCDM	Geometry-complete diffusion for 3D molecule generation and optimization	Small molecules	Link
11-Jul-24	AMPd-Up	De novoÿsynthetic antimicrobial peptide design with a recurrent neural network	AMPs	Link
26-Jul-24	PIDiff	PIDiff: Physics informed diffusion model for protein pocket-specific 3D molecular generation	Small molecules	Link
26-Jul-24	DrugHIVE	Structure-Based Drug Design with a Deep Hierarchical Generative Model	Small molecules	Link
25-Sep-24	PPFlow	PPFlow: Target-Aware Peptide Design with Torsional Flow Matching	Peptides	Link
1-Oct-24	BindCraft	BindCraft: one-shot design of functional protein binders	Protein design	Link
9-Oct-24	SCUBA-D	De novo protein design with a denoising diffusion network independent of pretrained structure prediction models	Protein design	Link
8-Nov-24	DeepBlock	A deep learning approach for rational ligand generation with toxicity control via reactive building blocks	Small molecules	Link
15-Nov-24	MPOGAN	A Multi-Property Optimizing Generative Adversarial Network for de novo Antimicrobial Peptide Design	AMPs	Link
4-Dec-24	3DSMILES-GPT	3DSMILES-GPT: 3D molecular pocket-based generation with token-only large language model	Small molecules	Link
4-Dec-24	TargetSA	TargetSA: adaptive simulated annealing for target-specific drug design	Small molecules	Link
9-Dec-24	DiffSBDD	Structure-based drug design with equivariant diffusion models	Small molecules	Link
12-Dec-24	TG-CDDPM	TG-CDDPM: text-guided antimicrobial peptides generation based on conditional denoising diffusion probabilistic model	AMPs	Link
15-Dec-24	PocketGen	Efficient generation of protein pockets with PocketGen	Protein pockets	Link
19-Dec-24	DiffInt	DiffInt: A Diffusion Model for Structure-Based Drug Design with Explicit Hydrogen Bond Interaction Guidance	Small molecules	Link
27-Jan-25	Prot2Drug	Transformer Decoder Learns from a Pretrained Protein Language Model to Generate Ligands with High Affinity	Small molecules	Link
5-Feb-25	PepDiffusion	Artificial intelligence using a latent diffusion model enables the generation of diverse and potent antimicrobial peptides	AMPs	Link
11-Mar-25	TransPharmer	Accelerating discovery of bioactive ligands with pharmacophore-informed generative models	Small molecules	Link
13-Mar-25	AMP-GAN	Exploring the repository of de novo-designed bifunctional antimicrobial peptides through deep learning	AMPs	Link
15-Mar-25	CMD-GEN	A structure-based framework for selective inhibitor design and optimization	Small molecules	Link
6-Apr-25	Boltzdesign1	Boltzdesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design	Protein design	Link
18-Apr-25	MolSnapper	MolSnapper: Conditioning Diffusion for Structure-Based Drug Design	Small molecules	Link
30-May-25	DeepDTAGen	DeepDTAGen: a multitask deep learning framework for drug-target affinity prediction and target-aware drugs generation	Small molecules	Link
5-Jul-25	FoldCraft	Fold-Conditioned De Novo Binder Design via AlphaFold2-Multimer Hallucination	Protein design	Link
10-Jul-25	ProtoBind-Diff	ProtoBind-Diff: A Structure-Free Diffusion Language Model for Protein Sequence-Conditioned Ligand Design	Small molecules	Link
1-Feb-25	AMP-diffusion	Generative latent diffusion language modeling yields anti-infective synthetic peptides	AMPs	Link
27-Mar-25	AIPAMPDS	AIPAMPDS: an AI platform for antimicrobial peptide design and screening	AMPs	Link