Department Publications

2024

29. CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson’s Disease Associated Protein

    Fengling Li, Suzanne Ackloo, Cheryl H. Arrowsmith, Fuqiang Ban, Christopher J. Barden, Hartmut Beck, … Dennis Della Corte, … Spencer S Gardiner^‡, … Austin J Jarrett^‡, … Connor J Morris^‡, … Damon Tingey^‡, … (85 other authors)

    J. Chem Inf. Model. 64 (22), 8521-8536 (2024).
    
30. Equipping Future Physicians with Artificial Intelligence Competencies through Student Associations

    Spencer Hopson^‡, Carson Mildon^‡, Kyle Hassard^‡, Paul M. Urie, and Dennis Della Corte

    Int. Med. Educ. 3 (4), 388-394 (2024).
    
31. Development of a national database for dietary glycemic index and load for nutritional epidemiologic studies in the United States

    Karen A. Della Corte, Dennis Della Corte, Sean Titensor^‡, Bo Yang, and Simin Liu

    Am. J. Clin. Nutr. 120 (2), 380-388 (2024).
    
32. Rise of the Allotrope Simple Model: Update from 2023 Fall Allotrope Connect

    Spencer Gardiner^‡, Christopher Haynie^‡, and Dennis Della Corte

    Drug Discov. Today 29 (4), 103944 (2024).
    

2023

25. TrIP─Transformer Interatomic Potential Predicts Realistic Energy Surface Using Physical Bias

    Bryce E. Hedelius^†, Damon Tingey^‡, and Dennis Della Corte

    J. Chem. Theory Comput. 20 (1), 199-211 (2023).
    
26. A probabilistic view of protein stability, conformational specificity, and design

    Jacob A. Stern^†, Tyler J. Free^†, Kimberlee L. Stern^†, Spencer Gardiner^‡, Nicholas A. Dalley^‡, Bradley C. Bundy, … and Dennis Della Corte (2 other authors)

    Sci. Rep. 13, 15493 (2023).
    
27. Towards a Clinically Useful AI Tool for Prostate Cancer Detection: Recommendations from a PANDA Dataset Analysis

    T. J. Hart^‡, Chloe Engler Hart^‡, Aaryn S. Frewing^‡, Paul M. Urie, and Dennis Della Corte

    JCRMHS , (2023).
    
28. Don't Fear the Artificial Intelligence: A Systematic Review of Machine Learning for Prostate Cancer Detection in Pathology

    Aaryn Frewing^‡, Alexander B. Gibson^‡, Richard Robertson^‡, Paul M. Urie, and Dennis Della Corte

    Arch. Pathol. Lab. Med. 148 (5), 603-612 (2023).
    

2022

21. MILCDock: Machine Learning Enhanced Consensus Docking for Virtual Screening in Drug Discovery

    Connor J. Morris^‡, Jacob A. Stern^†, Brenden Stark^‡, Max Christopherson^‡, and Dennis Della Corte

    J. Chem Inf. Model. 62 (22), 5342-5350 (2022).
    
22. Student-Created Video Content for Assessment and Experiential Learning

    Ben Graul^‡, Matthew L. Rollins^‡, Nathan Powers, and Dennis Della Corte

    Phys. Teach. 60 (6), 491-495 (2022).
    
23. Training undergraduate research assistants with an outcome-oriented and skill-based mentoring strategy

    Dennis Della Corte, Connor J. Morris^‡, Wendy M. Billings^‡, Jacob Stern^‡, Austin J. Jarrett^‡, Bryce Hedelius^†, and Adam Bennion

    Acta Crystallogr. Sect. D-Struct. Biol. 78 (8), (2022).
    
24. Computational methods to simulate molten salt thermophysical properties

    Talmage Porter^‡, Michael M. Vaka^‡, Parker Steenblik^‡, and Dennis Della Corte

    Comm. Chem. 5 (1), 69 (2022).
    
25. Self-reporting data assets and their representation in the pharmaceutical industry

    Dennis Della Corte, Wolfgang Colsman, Heiko Fessenmayr, Alexandre Sawczuk da Silva, and Dana E. Vanderwall

    Drug Discov. Today 27 (1), 207-214 (2022).
    

2021

16. Learning Small Molecule Energies and Interatomic Forces with an Equivariant Transformer on the ANI-1x Dataset

    Bryce Hedelius^‡, Fabian B. Fuchs, and Dennis Della Corte

    ELLIS Machine Learning for Molecule Discovery Workshop (2021).
    
17. Evaluation of Deep Neural Network ProSPr for Accurate Protein Distance Predictions on CASP14 Targets

    Jacob Stern^†, Bryce Hedelius^‡, Olivia Fisher^‡, Wendy M. Billings^‡, and Dennis Della Corte

    Int. J. Mol. Sci. 22, 12835 (2021).
    
18. Delivering Digital Transformation with Self-reporting Data Assets

    Dennis Della Corte, Naomi Young^‡, and Karen A. Della Corte

    Proceedings of the Future Technologies Conference (FTC) 2021, Volume 1. FTC 2021. Lecture Notes in Networks and Systems, vol 358. Springer, Cham.
    
19. Modeling SARS-CoV2 proteins in the CASP-commons experiment

    Andriy Kryshtafovych, John Moult, Wendy M. Billings^‡, Dennis Della Corte, Krzysztof Fidelis, Sohee Kwon, … (4 other authors)

    Proteins: Struct., Funct., Bioinf. , (2021).
    
20. The Data-Centric Lab: A Pharmaceutical Perspective

    Dennis Della Corte and Karen A. Della Corte

    Proceedings of the 2021 Future of Information and Communication Conference (FICC), pp 1-15, (2021).
    
21. The whole is greater than its parts: ensembling improves protein contact prediction

    Wendy M. Billings^‡, Connor J. Morris^‡, and Dennis Della Corte

    Sci. Rep. 11 (1), 8039 (2021).
    
22. Coming of age of allotrope: proceedings from the Fall 2020 Allotrope Connect

    Todd Millecam^‡, Austin J. Jarrett^‡, Naomi Young^‡, Dana E. Vanderwall, and Dennis Della Corte

    Drug Discov. Today 26 (8), 1922-1928 (2021).
    
23. Using molecular docking and molecular dynamics to investigate protein-ligand interactions

    Connor J. Morris^‡ and Dennis Della Corte

    Mod. Phys. Lett. B 35 (8), 2130002 (2021).
    
24. Current computational methods for enzyme design

    Talmage L. Coates^‡, Naomi Young^‡, Austin J. Jarrett^‡, Connor J. Morris^‡, James D. Moody, and Dennis Della Corte

    Mod. Phys. Lett. B 35 (9), 2150155 (2021).
    

2020

7. World trends in sugar-sweetened beverage and dietary sugar intakes in children and adolescents: a systematic review

   Karen Della Corte, Jessica Fife^†, Alexis Gardner, Britta L Murphy^†, Linda Kleis, Dennis Della Corte, … (3 other authors)

   Nutr. Rev. 79 (3), 274-288 (2020).
   
8. Engineering and application of a biosensor with focused ligand specificity

   Dennis Della Corte, Hugo L. van Beek, Falk Syberg, Marcus Schallmey, Felix Tobola, Kai U. Cormann, … Connor J. Morris^‡, … (8 other authors)

   Nat. Commun. 11 (1), 4851 (2020).
   
9. Context-dependent stabilizing interactions among solvent-exposed residues along the surface of a trimeric helix bundle

   Kimberlee L. Stern^†, Mason S. Smith^†, Wendy M. Billings^‡, Taylor J. Loftus^‡, Benjamin M. Conover^‡, Dennis Della Corte, and Joshua L. Price

   Biochemistry 59 (17), 1672-1679 (2020).
   
10. Library eArchiving with ZONTAL Space and the Allotrope Data Format

    Dennis Della Corte, Wolfgang Colsman, Ben Welker, and Brian Rennick

    Digital Library Perspectives 36 (1), (2020).
    

2018

3. Integrated NMR, Fluorescence and MD Benchmark Study of Protein Mechanics and Hydrodynamics

   Christina Möckel, Jakub Kubiak, Oliver Schillinger, Ralf Kuehnemuth, Dennis Della Corte, Gunnar F. Schröder, … (4 other authors)

   J. Phys. Chem. B 123 (7), 1453-1480 (2018).
   

2015

2. Coupling an Ensemble of Homologues Improves Refinement of Protein Homology Models

   André Wildberg, Dennis Della Corte, and Gunnar F. Schröder

   J. Chem. Theory Comput. 11 (12), 5578-5582 (2015).
   
3. Protein structure refinement with adaptively restrained homologous replicas

   Dennis Della Corte, André Wildberg, and Gunnar F. Schröder

   Eleventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (September 2016). Proteins: Struct., Funct., Bioinf. 84 (S1), (2015).
   

^‡Undergraduate Student Author

^†Graduate Student Author