BindGPT formulates 3D molecular design as autoregressive text generation over combined SMILES and XYZ tokens, using large-scale pre-training and reinforcement learning to achieve competitive pocket-conditioned molecule generation.
A minireview of chemical language models for de novo molecule design, covering SMILES and SELFIES representations, RNN and Transformer architectures, distribution learning, goal-directed and conditional generation, and prospective experimental validation.
CogMol uses a SMILES VAE and multi-attribute controlled sampling (CLaSS) to generate novel, target-specific drug molecules for unseen SARS-CoV-2 proteins without model retraining.
Introduces curriculum learning to the REINVENT de novo design platform, decomposing complex drug design objectives into simpler sequential tasks that accelerate agent convergence and improve output quality over standard reinforcement learning.
DrugEx v3 extends scaffold-constrained drug design by introducing a Graph Transformer with adjacency-matrix-based positional encoding, achieving 100% molecular validity and high predicted affinity for adenosine A2A receptor ligands.
An evolutionary molecular design framework that evolves ECFP fingerprint vectors using a genetic algorithm, reconstructs valid SMILES via an RNN decoder, and evaluates fitness with a DNN property predictor.
This survey organizes generative AI for de novo drug design into two themes: small molecule generation (target-agnostic, target-aware, conformation) and protein generation (structure prediction, sequence generation, backbone design, antibody, peptide). It covers four generative model families (VAEs, GANs, diffusion, flow-based), catalogs key datasets and benchmarks, and provides 12 comparative benchmark tables across all subtasks.
A foundational review surveying how deep generative models (VAEs, GANs, reinforcement learning) enable inverse molecular design, covering molecular representations, chemical space navigation, and applications from drug discovery to materials engineering.
Lingo3DMol introduces FSMILES, a fragment-based SMILES representation with local and global coordinates, to generate drug-like 3D molecules in protein pockets via a transformer language model.
Link-INVENT is an RNN-based generative model for molecular linker design that uses reinforcement learning with a flexible scoring function, demonstrated on fragment linking, scaffold hopping, and PROTAC design.
Demonstrates that standard transformer language models, trained with next-token prediction on sequences from XYZ, CIF, and PDB files, can generate valid 3D molecules, crystals, and protein binding sites competitive with domain-specific 3D generative models.
PASITHEA adapts deep dreaming from computer vision to molecular design, directly optimizing SELFIES-encoded molecules for target chemical properties via gradient-based inversion of a trained regression network.