David Ryan Koes

1. Improvements to the APBS biomolecular solvation software suite
   2017/08/24 by Elizabeth Jurrus, Dave Engel, Keith Star +28 · 32 citations
   Biochemistry, Genetics and Molecular Biology · #Advanced Fluorescence Microscopy Techniques #Gene Regulatory Network Analysis #Protein Structure and Dynamics
2. Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models
   2021/10/28 by Matthew Ragoza, Tomohide Masuda, Ragoza, Matthew +3 · 15 citations
   Biochemistry, Genetics and Molecular Biology · Computer Science · #Chemical Synthesis and Analysis #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM)
3. Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation
   2024/04/30 by Ian Dunn, Dunn, Ian, David Ryan Koes +1 · 17 citations
   Computer Science · Engineering · #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Computer and information sciences #Innovative Microfluidic and Catalytic Techniques Innovation #Machine Learning (cs.LG) #Machine Learning and Data Classification #Statistical and Computational Modeling
4. Learning a Continuous Representation of 3D Molecular Structures with\n Deep Generative Models
   2020/10/16 by Matthew Ragoza, Ragoza, Matthew, Tomohide Masuda +3 · 7 citations
   Biochemistry, Genetics and Molecular Biology · Computer Science · Materials Science · #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #Graph Theory and Algorithms #Machine Learning (cs.LG) #Machine Learning in Materials Science #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM)
5. Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models
   2020/10/16 by Tomohide Masuda, Masuda, Tomohide, Matthew Ragoza +3 · 2 citations
   Biochemistry, Genetics and Molecular Biology · Computer Science · #Biomolecules (q-bio.BM) #Chemical Physics (physics.chem-ph) #Chemical Synthesis and Analysis #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #FOS: Physical sciences #Machine Learning (cs.LG) #Protein Structure and Dynamics
6. SidechainNet: An All-Atom Protein Structure Dataset for Machine Learning
   2020/10/16 by Jonathan King, David Ryan Koes, King, Jonathan E. +1 · 2 citations
   Biochemistry, Genetics and Molecular Biology · Computer Science · Materials Science · #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning in Materials Science #Protein Structure and Dynamics
7. Scaling Structure Aware Virtual Screening to Billions of Molecules with SPRINT
   2024/11/23 by Andrew T. McNutt, Abhinav Adduri, Abhinav K. Adduri +13 · 3 voices · 2 citations
   Chemistry · #Advanced Proteomics Techniques and Applications #cs.LG #q-bio.BM
8. libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications
   2019/12/10 by Jocelyn Sunseri, David Ryan Koes, Sunseri, Jocelyn +1 · 1 citation
   Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · Materials Science · #Biomolecules (q-bio.BM) #Chemical Physics (physics.chem-ph) #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #FOS: Physical sciences #Machine Learning (cs.LG) #Machine Learning in Materials Science #Molecular spectroscopy and chirality #Protein Structure and Dynamics
9. GNINA 1.3: the next increment in molecular docking with deep learning
   2025/03/02 by Andrew T. McNutt, Yanjing Li, Rocco Meli +2 · 1 voice · 3 citations
   Chemistry · Computer Science · #Click Chemistry and Applications #Computational Drug Discovery Methods #Synthesis and biological activity
10. BoltzNCE: Learning Likelihoods for Boltzmann Generation with Stochastic Interpolants and Noise Contrastive Estimation
    2025/07/01 by Rishal Aggarwal, Aggarwal, Rishal, Jacky Chen +5 · 1 voice · 2 citations
    #cs.LG #physics.bio-ph
11. Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure
    2023/11/22 by Ian Dunn, Dunn, Ian, David Ryan Koes +1 · 2 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · Materials Science · #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning in Materials Science #Protein Structure and Dynamics