Computational and Computer Aided Drug Design (CAAD) Articles
Spiegel, J.O., Durrant, J.D. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. J Cheminform 12, 25 (2020). http://doi.org/ggwwcp Download PDF
Cheminformatic Articles
Ropp, P.J., Spiegel, J.O., et al. Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. J Cheminform 11, 34 (2019). http://doi.org/gf48dh Download PDF
Ph.D. Dissertation
Spiegel, J.O., (2020) Targeting the Poly (ADP-Ribose) Polymerase-1 Catalytic Pocket Using AutoGrow4, a Genetic Algorithm for de novo Design. Doctoral Dissertation, University of Pittsburgh. http://d-scholarship.pitt.edu/39666/ Download PDF
Patents
Spiegel, J.O., Lalwani, G., Toussaint, J., Patel, S., Sitharaman, B. (2013). Synthesis of Graphene Via Hydro-Jets. US Provisional Application, OTLIR, Stony Brook University
Aknowledged Contributions
Lab Informatics & Data Ontology
Kappler, M., Lowden, C. and Culberson, J. (2022) BioChemUDM: a unified data model for compounds and assays. Pure and Applied Chemistry, Vol. 94 (Issue 6), pp. 737-744. https://doi.org/10.1515/pac-2021-1004 Download PDF
Molecular Dynamics and Protein Visualization
Durrant, J. D. (2019). Blendmol: Advanced macromolecular visualization in Blender. Bioinformatics, 35(13), 2323–2325. https://doi.org/10.1093/bioinformatics/bty968 Download PDF
Articles in Preparation
Spiegel, J.O., O’Donnell, A., Durrant, J.D., (2023). Molecular Dynamics of α-arrestin TXNIP.
Spiegel, J.O., Durrant, J.D., Bowman, R., O’Donnell, A. (2023). Putting the Brakes on α-arrestin Trafficking: α-arrestin Regulation by Phosphorylation and Ubiquitination.
Mayo, E., Spiegel, J.O., J.O., Durrant, J.D., Ochoa, E., (2023). Evaluation of metalloprotein docking using Plasmodium falciparum PfA-M1 aminopeptidase.
Spiegel, J.O., Lowden, C., (2023). A novel approach for heterocyclic regioisomer enumeration.