De Novo Design Tools
LiGAN
Date: 7-Feb-22
Paper: Generating 3D molecules conditional on receptor binding sites with deep generative models
Task: Small molecules
DOI: https://doi.org/10.1039/D1SC05976A
Code: https://github.com/mattragoza/liGAN
Pocket2Mol
Date: 15-May-22
Paper: Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
Task: Small molecules
DOI: https://doi.org/10.48550/arXiv.2205.07249
Code: https://github.com/pengxingang/Pocket2Mol
ProteinMPNN
Date: 15-Sep-22
Paper: Robust deep learning based protein sequence design using ProteinMPNN
Task: Protein design
DOI: https://doi.org/10.1126/science.add2187
Code: https://github.com/dauparas/ProteinMPNN
AlphaDrug
Date: 7-Oct-22
Paper: AlphaDrug: protein target specific de novo molecular generation
Task: Small molecules
DOI: https://doi.org/10.1093/pnasnexus/pgac227
Code: https://github.com/CMACH508/AlphaDrug
FrameDiff
Date: 5-Feb-23
Paper: SE(3) diffusion model with application to protein backbone generation
Task: Protein design
DOI: https://doi.org/10.48550/arXiv.2302.02277
Code: https://github.com/jasonkyuyim/se3_diffusion
RFDiffudion
Date: 11-Jul-23
Paper: De novo design of protein structure and function with RFdiffusion
Task: Protein design
DOI: https://doi.org/10.1038/s41586-023-06415-8
Code: https://github.com/RosettaCommons/RFdiffusion
DiffHopp
Date: 14-Aug-23
Paper: DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping
Task: Small molecules
DOI: https://doi.org/10.48550/arXiv.2308.07416
Code: https://github.com/jostorge/diffusion-hopping
ResGen
Date: 7-Sep-23
Paper: ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling
Task: Small molecules
DOI: https://doi.org/10.1038/s42256-023-00712-7
Code: https://github.com/HaotianZhangAI4Science/ResGen
LinkerNet
Date: 22-Sep-23
Paper: LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion
Task: Fragments linking
DOI: https://openreview.net/forum?id=6EaLIw3W7c
Code: https://github.com/guanjq/LinkerNet
KGDiff
Date: 1-Dec-23
Paper: KGDiff: towards explainable target-aware molecule generation with knowledge guidance
Task: Small molecules
DOI: https://doi.org/10.1093/bib/bbad435
Code: https://github.com/CMACH508/KGDiff
Lingo3DMol
Date: 15-Jan-24
Paper: Generation of 3D molecules in pockets via a language model
Task: Small molecules
DOI: https://doi.org/10.1038/s42256-023-00775-6
Code: https://github.com/stonewiseAIDrugDesign/Lingo3DMol
DiffDec
Date: 24-Jan-24
Paper: DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model
Task: Small molecules
DOI: https://doi.org/10.1021/acs.jcim.3c01466
Code: https://github.com/biomed-AI/DiffDec
Foldingdiff
Date: 5-Feb-24
Paper: Protein structure generation via folding diffusion
Task: Protein design
DOI: https://doi.org/10.1038/s41467-024-45051-2
Code: https://github.com/microsoft/foldingdiff
PocketFlow
Date: 11-Mar-24
Paper: PocketFlow is a data-and-knowledge-driven structure-based molecular generative model
Task: Small molecules
DOI: https://doi.org/10.1038/s42256-024-00808-8
Code: https://github.com/Saoge123/PocketFlow
SyntheMol
Date: 22-Mar-24
Paper: Generative AI for designing and validating easily synthesizable and structurally novel antibiotics
Task: Small molecules
DOI: https://doi.org/10.1038/s42256-024-00809-7
Code: https://github.com/swansonk14/SyntheMol
PMDM
Date: 26-Mar-24
Paper: A dual diffusion model enables 3D molecule generation and lead optimization based on target pockets
Task: Small molecules
DOI: https://doi.org/10.1038/s41467-024-46569-1
Code: https://github.com/Layne-Huang/PMDM/tree/main
DeepICL
Date: 27-Mar-24
Paper: 3D molecular generative framework for interaction-guided drug design
Task: Small molecules
DOI: https://doi.org/10.1038/s41467-024-47011-2
Code: https://github.com/ACE-KAIST/DeepICL
DiffLinker
Date: 11-Apr-24
Paper: Equivariant 3D-conditional diffusion model for molecular linker design
Task: Fragments linking
DOI: https://doi.org/10.1038/s42256-024-00815-9
Code: https://github.com/igashov/DiffLinker
dragonfly_gen
Date: 22-Apr-24
Paper: Prospective de novo drug design with deep interactome learning
Task: Small molecules
DOI: https://doi.org/10.1038/s41467-024-47613-w
Code: https://github.com/ETHmodlab/dragonfly_gen
ChemoDOTS
Date: 30-Apr-24
Paper: ChemoDOTS: a web server to design chemistry-driven focused libraries
Task: Small molecules
DOI: https://doi.org/10.1093/nar/gkae326
Code: https://github.com/iSCBTeam/ChemoDOTS
SynFlowNet
Date: 2-May-24
Paper: SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints
Task: Small molecules
DOI: https://doi.org/10.48550/arXiv.2405.01155
Code: https://github.com/mirunacrt/synflownet
GCDM
Date: 3-Jul-24
Paper: Geometry-complete diffusion for 3D molecule generation and optimization
Task: Small molecules
DOI: https://doi.org/10.1038/s42004-024-01233-z
Code: https://github.com/BioinfoMachineLearning/Bio-Diffusion
AMPd-Up
Date: 11-Jul-24
Paper: De novoÿsynthetic antimicrobial peptide design with a recurrent neural network
Task: AMPs
DOI: https://doi.org/10.1002/pro.5088
Code: https://github.com/bcgsc/AMPd-Up
PIDiff
Date: 26-Jul-24
Paper: PIDiff: Physics informed diffusion model for protein pocket-specific 3D molecular generation
Task: Small molecules
DOI: https://doi.org/10.1016/j.compbiomed.2024.108865
Code: https://github.com/hello-maker/PIDiff
DrugHIVE
Date: 26-Jul-24
Paper: Structure-Based Drug Design with a Deep Hierarchical Generative Model
Task: Small molecules
DOI: https://doi.org/10.1021/acs.jcim.4c01193
Code: https://github.com/jssweller/DrugHIVE
PPFlow
Date: 25-Sep-24
Paper: PPFlow: Target-Aware Peptide Design with Torsional Flow Matching
Task: Peptides
DOI: https://doi.org/10.1101/2024.03.07.583831
Code: https://github.com/Edapinenut/ppflow
BindCraft
Date: 1-Oct-24
Paper: BindCraft: one-shot design of functional protein binders
Task: Protein design
DOI: https://doi.org/10.1101/2024.09.30.615802
Code: https://github.com/martinpacesa/BindCraft
SCUBA-D
Date: 9-Oct-24
Paper: De novo protein design with a denoising diffusion network independent of pretrained structure prediction models
Task: Protein design
DOI: https://doi.org/10.1038/s41592-024-02437-w
Code: https://github.com/liuyf020419/SCUBA-D
DeepBlock
Date: 8-Nov-24
Paper: A deep learning approach for rational ligand generation with toxicity control via reactive building blocks
Task: Small molecules
DOI: https://doi.org/10.1038/s43588-024-00718-0
Code: https://github.com/BioChemAI/DeepBlock
MPOGAN
Date: 15-Nov-24
Paper: A Multi-Property Optimizing Generative Adversarial Network for de novo Antimicrobial Peptide Design
Task: AMPs
DOI: https://doi.org/10.1101/2024.11.13.623386
Code: https://github.com/23AIBox/MPOGAN
3DSMILES-GPT
Date: 4-Dec-24
Paper: 3DSMILES-GPT: 3D molecular pocket-based generation with token-only large language model
Task: Small molecules
DOI: https://doi.org/10.1039/D4SC06864E
Code: https://github.com/ashipiling/GPT_3DSMILES
TargetSA
Date: 4-Dec-24
Paper: TargetSA: adaptive simulated annealing for target-specific drug design
Task: Small molecules
DOI: https://doi.org/10.1093/bioinformatics/btae730
Code: https://github.com/XueZhe-Zachary/TargetSA
DiffSBDD
Date: 9-Dec-24
Paper: Structure-based drug design with equivariant diffusion models
Task: Small molecules
DOI: https://doi.org/10.1038/s43588-024-00737-x
Code: https://github.com/arneschneuing/DiffSBDD
TG-CDDPM
Date: 12-Dec-24
Paper: TG-CDDPM: text-guided antimicrobial peptides generation based on conditional denoising diffusion probabilistic model
Task: AMPs
DOI: https://doi.org/10.1093/bib/bbae644
Code: https://github.com/JunhangCao/TG-CDDPM
PocketGen
Date: 15-Dec-24
Paper: Efficient generation of protein pockets with PocketGen
Task: Protein pockets
DOI: https://doi.org/10.1038/s42256-024-00920-9
Code: https://github.com/zaixizhang/PocketGen
DiffInt
Date: 19-Dec-24
Paper: DiffInt: A Diffusion Model for Structure-Based Drug Design with Explicit Hydrogen Bond Interaction Guidance
Task: Small molecules
DOI: https://doi.org/10.1021/acs.jcim.4c01385
Code: https://github.com/sekijima-lab/DiffInt
Prot2Drug
Date: 27-Jan-25
Paper: Transformer Decoder Learns from a Pretrained Protein Language Model to Generate Ligands with High Affinity
Task: Small molecules
DOI: https://doi.org/10.1021/acs.jcim.4c02019
Code: https://zenodo.org/records/14637195
PepDiffusion
Date: 5-Feb-25
Paper: Artificial intelligence using a latent diffusion model enables the generation of diverse and potent antimicrobial peptides
Task: AMPs
DOI: https://doi.org/10.1126/sciadv.adp7171
Code: https://github.com/Wangyj2023/PepDiffusion
TransPharmer
Date: 11-Mar-25
Paper: Accelerating discovery of bioactive ligands with pharmacophore-informed generative models
Task: Small molecules
DOI: https://doi.org/10.1038/s41467-025-56349-0
Code: https://github.com/iipharma/transpharmer-repo
AMP-GAN
Date: 13-Mar-25
Paper: Exploring the repository of de novo-designed bifunctional antimicrobial peptides through deep learning
Task: AMPs
DOI: https://doi.org/10.7554/eLife.97330.3
Code: https://github.com/ruihan-dong/GAN-for-AMP-Design
CMD-GEN
Date: 15-Mar-25
Paper: A structure-based framework for selective inhibitor design and optimization
Task: Small molecules
DOI: https://doi.org/10.1038/s42003-025-07840-3
Code: https://github.com/zyrlia1018/CMD-GEN
Boltzdesign1
Date: 6-Apr-25
Paper: Boltzdesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design
Task: Protein design
DOI: https://doi.org/10.1101/2025.04.06.647261
Code: https://github.com/yehlincho/BoltzDesign1
MolSnapper
Date: 18-Apr-25
Paper: MolSnapper: Conditioning Diffusion for Structure-Based Drug Design
Task: Small molecules
DOI: https://doi.org/10.1021/acs.jcim.4c02008
Code: https://github.com/oxpig/MolSnapper
DeepDTAGen
Date: 30-May-25
Paper: DeepDTAGen: a multitask deep learning framework for drug-target affinity prediction and target-aware drugs generation
Task: Small molecules
DOI: https://doi.org/10.1038/s41467-025-59917-6
Code: https://github.com/CSUBioGroup/DeepDTAGen
FoldCraft
Date: 5-Jul-25
Paper: Fold-Conditioned De Novo Binder Design via AlphaFold2-Multimer Hallucination
Task: Protein design
DOI: https://doi.org/10.1101/2025.07.02.662497
Code: https://github.com/KhondamirRustamov/FoldCraft
ProtoBind-Diff
Date: 10-Jul-25
Paper: ProtoBind-Diff: A Structure-Free Diffusion Language Model for Protein Sequence-Conditioned Ligand Design
Task: Small molecules
DOI: https://doi.org/10.1101/2025.06.16.659955
Code: https://github.com/gero-science/ProtoBind-Diff
AMP-diffusion
Date: 1-Feb-25
Paper: Generative latent diffusion language modeling yields anti-infective synthetic peptides
Task: AMPs
DOI: https://doi.org/10.1101/2025.01.31.636003
Code: https://github.com/programmablebio/amp-diffusion
AIPAMPDS
Date: 27-Mar-25
Paper: AIPAMPDS: an AI platform for antimicrobial peptide design and screening
Task: AMPs
DOI: https://doi.org/10.1101/2025.03.24.644774
Code: https://github.com/LYRHeidi/AIPAMPDS