Cover Image

Diffusion Models at the Drug Discovery Frontier: A Review on Generating Small Molecules versus Therapeutic Peptides

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Wang, Yiquan, Ma, Yahui, Chang, Yuhan, Yan, Jiayao, Zhang, Jialin, Cai, Minnuo, Wei, Kai
Format:	Preprint
Published:	2025
Subjects:	Machine Learning Artificial Intelligence Biomolecules Quantitative Methods
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation
by: Wang, Yongkang, et al.
Published: (2023)

Leveraging Machine Learning Models for Peptide-Protein Interaction Prediction
by: Yin, Song, et al.
Published: (2023)

Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks
by: Ünlü, Atabey, et al.
Published: (2023)

Explainable Machine Learning and Deep Learning Models for Predicting TAS2R-Bitter Molecule Interactions
by: Ferri, Francesco, et al.
Published: (2024)

Designing the Haystack: Programmable Chemical Space for Generative Molecular Discovery
by: Zhu, Yuchen, et al.
Published: (2026)

NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation
by: Liu, Zhiyuan, et al.
Published: (2025)

Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization
by: Gu, Siyi, et al.
Published: (2024)

ProDCARL: Reinforcement Learning-Aligned Diffusion Models for De Novo Antimicrobial Peptide Design
by: Sheng, Fang, et al.
Published: (2026)

Marginal Girsanov Reweighting: Stable Variance Reduction for Long-Timescale Dynamics from Biased Simulation
by: Wang, Yan, et al.
Published: (2025)

Scoring-Assisted Generative Exploration for Proteins (SAGE-Prot): A Framework for Multi-Objective Protein Optimization via Iterative Sequence Generation and Evaluation
by: Lim, Hocheol, et al.
Published: (2025)

Characterizing the Conformational States of G Protein Coupled Receptors Generated with AlphaFold
by: Chib, Garima, et al.
Published: (2025)

AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information
by: Xia, Jun, et al.
Published: (2024)

Apo2Mol: 3D Molecule Generation via Dynamic Pocket-Aware Diffusion Models
by: Zheng, Xinzhe, et al.
Published: (2025)

Protein folding classes -- High-dimensional geometry of amino acid composition space revisited
by: Mao, Boryeu
Published: (2025)

GoForth: Language Models for RNA Design under Structure, Sequence, and Coding Constraints
by: Lindsey, Michael
Published: (2026)

Benchmarking structure-based three-dimensional molecular generative models using GenBench3D: ligand conformation quality matters
by: Baillif, Benoit, et al.
Published: (2024)

Canonicalization of the E value from BLAST similarity search -- dissimilarity measure and distance function for a metric space of protein sequences
by: Mao, Boryeu
Published: (2025)

Frequency-Space Mechanics: A Sequence and Coordinate-Free Representation for Protein Function Prediction
by: Reilly, Charles B
Published: (2026)

AntiFold: Improved antibody structure-based design using inverse folding
by: Høie, Magnus Haraldson, et al.
Published: (2024)

HelixVS: Deep Learning-Enhanced Structure-Based Platform for Screening and Design
by: Zhang, Shanzhuo, et al.
Published: (2025)

EscalNet: Learn isotropic representation space for biomolecular dynamics based on effective energy
by: Zuo, Guanghong
Published: (2025)

Network Pharmacology Framework Characterizes Polypharmacological Properties of Dietary Flavonoids: Integration of Computational, Experimental, and Epidemiological Evidence
by: Fujisaki, Koyo, et al.
Published: (2026)

Persistent Sheaf Laplacian Analysis of Protein Flexibility
by: Hayes, Nicole, et al.
Published: (2025)

Raman Spectroscopy Reveals Photobiomodulation-Induced α-Helix to β-Sheet Transition in Tubulins: Potential Implications for Alzheimer's and Other Neurodegenerative Diseases
by: Di Gregorio, Elisabetta, et al.
Published: (2023)

mRNA Folding Algorithms for Structure and Codon Optimization
by: Ward, Max, et al.
Published: (2025)

Two for the Price of One: Integrating Large Language Models to Learn Biophysical Interactions
by: Clark, Joseph D., et al.
Published: (2025)

Quantifying the uncertainty of molecular dynamics simulations : Good-Turing statistics revisited
by: Tsampazi, Vasiliki, et al.
Published: (2026)

Predicting Protein-Nucleic Acid Flexibility Using Persistent Sheaf Laplacians
by: Hayes, Nicole, et al.
Published: (2025)

Quantification of protein homodimer affinity using native mass spectrometry
by: Schulte, Jonathan, et al.
Published: (2025)

Conformational landscapes in cryo-ET data based on MD simulations
by: Jonic, Slavica
Published: (2026)

Combining oligo pools and Golden Gate cloning to create protein variant libraries or guide RNA libraries for CRISPR applications
by: Valero, Alicia Maciá, et al.
Published: (2024)

Non-perturbative Bacterial Identification Directly from Solid Agar Plates Using Raman
by: Kim, Jeong Hee, et al.
Published: (2026)

VARIANT: Web Server for Decoding and Analyzing Viral Mutations at Genome and Protein Levels
by: Wang, Rui, et al.
Published: (2026)

Substrate Prediction for RiPP Biosynthetic Enzymes via Masked Language Modeling and Transfer Learning
by: Clark, Joseph D., et al.
Published: (2024)

Impact of Force Field Polarization on Correlated Motions of Proteins
by: Milinski, Ana, et al.
Published: (2025)

Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins
by: Ghafouri, Hamidreza, et al.
Published: (2025)

LAFA: A Framework for Reproducible Longitudinal Assessment of Protein Function Annotation Models
by: Phan, An, et al.
Published: (2026)

Benchmarking open-source tools for in silico antiviral drug discovery
by: Elton, Daniel C., et al.
Published: (2026)

Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design
by: Liu, Shengchao, et al.
Published: (2024)

Pharmacology Knowledge Graphs: Do We Need Chemical Structure for Drug Repurposing?
by: Abo-Dahab, Youssef, et al.
Published: (2026)