arXiv:2607. 00947v1 Announce Type: new Abstract: Generative models learn data distributions that reside on a low-dimensional manifold within a higher-dimensional ambient space.
By Ludwig Winkler, Andrew Leaver-Fay, Joseph Kleinhenz, Pan Kessel
arXiv:2606. 19377v1 Announce Type: cross Abstract: Computational enzyme design requires generating proteins that scaffold catalytic residues and ligands, a task that demands both geometric accuracy and structural diversity from the underlying generative model.
By Nicholas J. Williams, Ward Haddadin, Matteo P. Ferla, Constantin Schneider, Nicholas B. Woodall, Ruby Sedgwick, Christian D. Madsen, Andrew L. Hopkins, Edward O. Pyzer-Knapp
arXiv:2504. 02839v2 Announce Type: replace-cross Abstract: Proteins move and deform to ensure their biological functions.
By Valentin Lombard, Julien Nguyen Van, Sergei Grudinin, Elodie Laine
arXiv:2606. 08375v1 Announce Type: new Abstract: All-atom generative modeling of 3D biomolecular complexes has emerged as the dominant paradigm for predicting the structure of proteins and protein-ligand systems.
By Gianluca Scarpellini, Ron Shprints, Peter Holderrieth, Juno Nam, Pranav Murugan, Rafael G\'omez-Bombarelli, Tommi Jaakola, Maruan Al-Shedivat, Nicholas Matthew Boffi, Avishek Joey Bose
arXiv:2606. 11243v1 Announce Type: new Abstract: De novo protein generation has transformative potential in therapeutic design, enzyme engineering, and synthetic biology.
By Chuanzhen Wang, Meade Cleti, Pete Jano
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.
By Benno Kaech, Luis Wyss, Karsten Borgwardt, Gianvito Grasso