arXiv:2604.18467v3 Announce Type: replace-cross Abstract: Motivation: Peptide-protein interactions (PepPIs) are central to cellular regulation and peptide therapeutics, but experimental characterizat...
arXiv:2606. 27824v1 Announce Type: cross Abstract: Peptides are a promising therapeutic modality that combine the chemical tunability of small molecules with the target specificity of macromolecular therapeutics.
arXiv:2606. 12991v1 Announce Type: new Abstract: Cyclic peptides represent a promising class of therapeutic compounds in modern drug discovery, often offering improved stability and binding affinity.
arXiv:2608. 19808v1 Announce Type: new Abstract: Cyclic peptides are emerging as promising molecular scaffolds in drug discovery due to their high binding affinity and structural stability.
arXiv:2608.21367v1 Announce Type: cross Abstract: Protein-peptide interactions are central to cellular regulation and peptide-based drug discovery, yet existing computational methods mainly focus on...
arXiv:2607. 09039v1 Announce Type: new Abstract: The ability to generate variable-length proteins is crucial in protein design, where the optimal length is often unknown and tightly coupled to designability.
Cyclic peptides are emerging as promising molecular scaffolds in drug discovery due to their high binding affinity and structural stability. However, extending generative models from linear to cyclic...
arXiv:2504. 17247v3 Announce Type: replace Abstract: Deep learning-based antimicrobial peptide (AMP) discovery faces critical challenges such as limited controllability, lack of representations that efficiently model antimicrobial properties, and low experimental hit rates.
PocketVE is a protein-pocket-conditioned variance‑exploding diffusion framework that integrates stable 3D coordinate denoising, classifier‑free property guidance, and adaptive protein perturbation. It improves 3D validity from 58.6% to 80.6% and reduces strain energy from 457.4 to 127.9 on CrossDocked2020 while maintaining competitive docking and property scores. The study shows moderate guidance balances target objectives with geometric quality, and diagnostics confirm enhanced pocket compatibility.
arXiv:2509. 26405v2 Announce Type: replace Abstract: We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules.
arXiv:2606. 17127v1 Announce Type: cross Abstract: Antimicrobial resistance causes to over a million deaths annually.
arXiv:2606. 00555v1 Announce Type: new Abstract: Structure-based drug design increasingly employs LLM agents to iteratively refine ligands against a target pocket, yet a viable ligand must satisfy two often-conflicting objectives -- binding affinity and druggability -- which single optimization steps rarely improve together.