5 papers
Discontinuous Epitope Fragments as Sufficient Target Templates for Efficient Binder Design
Zhenfeng Deng, Ruijie Hou, Ningrui Xie +2
Recent advances in structure-based protein design have accelerated de novo binder generation, yet interfaces on large domains or spanning multiple domains remain challenging due to…
Measuring Scientific Capabilities of Language Models with a Systems Biology Dry Lab
Haonan Duan, Stephen Zhewen Lu, Caitlin Fiona Harrigan +5
Designing experiments and result interpretations are core scientific competencies, particularly in biology, where researchers perturb complex systems to uncover the underlying syst…
SynCoGen: Synthesizable 3D Molecule Generation via Joint Reaction and Coordinate Modeling
Andrei Rekesh, Miruna Cretu, Dmytro Shevchuk +6
Synthesizability remains a critical bottleneck in generative molecular design. While recent advances have addressed synthesizability in 2D graphs, extending these constraints to 3D…
Scalable and Cost-Efficient de Novo Template-Based Molecular Generation
Piotr Gaiński, Oussama Boussif, Andrei Rekesh +5
Template-based molecular generation offers a promising avenue for drug design by ensuring generated compounds are synthetically accessible through predefined reaction templates and…
Learning Decision Trees as Amortized Structure Inference
Mohammed Mahfoud, Ghait Boukachab, Michał Koziarski +4
Building predictive models for tabular data presents fundamental challenges, notably in scaling consistently, i.e., more resources translating to better performance, and generalizi…