arXiv AI
Jul 7
Folding, Reasoning, and Scaling with Open-source Drug Discovery Engine
arXiv:2607. 03787v1 Announce Type: new Abstract: Accurately modeling biomolecular interactions is a central bottleneck in biology and therapeutic discovery.
Vilya-1: An all-atom foundation model for macrocycle structure prediction and design
arXiv:2607. 09998v1 Announce Type: new Abstract: Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space.
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arXiv Machine Learning
Jun 25
Scalable Peptide Design via Memory-Efficient Equivariant Transformer
arXiv:2606. 25006v1 Announce Type: new Abstract: Target-specific peptide design requires sequence and structure co-design under full atom geometric constraints.
arXiv Machine Learning
Jul 1
ElemeNet: Multiscale Molecular Machine Learning with Uncertainty Quantification Across the Periodic Table
arXiv:2606. 30961v1 Announce Type: cross Abstract: Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species.
Hugging Face Trending Papers
Jun 23
Scalable Peptide Design via Memory-Efficient Equivariant Transformer
Target-specific peptide design requires sequence and structure co-design under full atom geometric constraints. Latent generative frameworks offer an effective route for this problem by compressing fine grained atomic structures into block level latent representations and performing conditional generation in a compact latent space.
arXiv Machine Learning
5d ago
WEECFP-SuRGE: A Position-Aware Substructure Encoding Method for Molecular Property Prediction
WEECFP-SuRGE introduces a position‑aware substructure encoding method that combines tokenized hierarchical Morgan fingerprints with graph‑distance‑dependent rotations applied at the input and within transformer self‑attention. The approach captures local chemistry, long‑range interactions, and molecular topology without requiring external pretraining or 3‑D conformer generation. Benchmarks on MoleculeNet and the Therapeutic Data Commons ADMET datasets show competitive performance, and a reconstruction procedure correctly identifies constitutional isomers for 92.6% of a 4,200‑molecule library.
arXiv Machine Learning
Jun 11
DeepRHP: A Hybrid Variational Autoencoder for Designing Random Heteropolymers as Protein Mimics
arXiv:2606. 11651v1 Announce Type: new Abstract: Synthetic random heteropolymers (RHPs), consisting of a predefined set of monomers, offer an approach toward the design of protein-like materials.
arXiv AI
2d ago
Higher-Order Molecular Grammars for Generative and Foundation Models in Chemistry
arXiv:2610.02186v1 Announce Type: cross Abstract: Molecular learning models are strongly shaped by their underlying representations. Yet standard sequential and graph formalisms struggle to explicitl...
arXiv Machine Learning
Jun 15
Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction
arXiv:2606. 14217v1 Announce Type: new Abstract: Accurate prediction of protein-ligand binding affinity is essential for structure-based drug discovery.
arXiv AI
Jul 24
SenCos-GEM: SENet-Calibrated and Law-of-Cosines-Constrained Geometry-Enhanced Molecular Representation for Property Prediction
arXiv:2607. 20551v1 Announce Type: cross Abstract: Effective molecular representation learning is crucial for accurate molecular property prediction.
arXiv Machine Learning
2d ago
EnsembleEGNN: Set-Based Graph Learning for Thermodynamic Ensembles of Cyclic Peptides
arXiv:2607.21561v2 Announce Type: replace Abstract: Molecular graph encoding often relies on a single, static structure, ignoring the thermodynamic ensemble of molecules that are present in solution....
arXiv AI
Aug 18
Protein Structure Prediction: From Evolutionary Constraints to Generative Modeling
arXiv:2608. 16094v1 Announce Type: new Abstract: Accurate protein structure prediction is fundamental to structural biology because protein structure underlies molecular function and provides a basis for mechanistic interpretation.
arXiv AI
Aug 5
Learning Molecular Representations from Cellular Phenotypes with Structure Preservation
arXiv:2608. 02688v1 Announce Type: cross Abstract: Phenotypic drug discovery enables the discovery of functional relationships between molecular structures and cellular responses.