The University of Queensland

AI-driven enhancements in drug screening and optimization

Serghini, Adam, Portelli, Stephanie and Ascher, David B. (2024). AI-driven enhancements in drug screening and optimization. Computational drug discovery and design. (pp. 269-294) edited by Mohini Gore and Umesh B. Jagtap. New York, NY, United States: Humana. doi: 10.1007/978-1-0716-3441-7_15

Identifying genotype-phenotype correlations via integrative mutation analysis

Airey, Edward, Portelli, Stephanie, Xavier, Joicymara S, Myung, Yoo Chan, Silk, Michael, Karmakar, Malancha, Velloso, João P L, Rodrigues, Carlos H M, Parate, Hardik H, Garg, Anjali, Al-Jarf, Raghad, Barr, Lucy, Geraldo, Juliana A, Rezende, Pâmela M, Pires, Douglas E V and Ascher, David B (2021). Identifying genotype-phenotype correlations via integrative mutation analysis. Artificial neural networks. (pp. 1-32) edited by Hugh Cartwright. New York, NY, United States: Humana. doi: 10.1007/978-1-0716-0826-5_1

A comprehensive computational platform to guide drug development using graph-based signature methods

Pires, Douglas E. V., Portelli, Stephanie, Rezende, Pâmela M., Veloso, Wandré N. P., Xavier, Joicymara S., Karmakar, Malancha, Myung, Yoochan, Linhares, João P. V., Rodrigues, Carlos H. M., Silk, Michael and Ascher, David B. (2020). A comprehensive computational platform to guide drug development using graph-based signature methods. Structural bioinformatics: methods and protocols. (pp. 91-106) New York, NY, United States: Humana. doi: 10.1007/978-1-0716-0270-6_7

Exploring protein supersecondary structure through changes in protein folding, stability, and flexibility

Pires, Douglas E. V., Rodrigues, Carlos H. M., Albanaz, Amanda T. S., Karmakar, Malancha, Myung, Yoochan, Xavier, Joicymara, Michanetzi, Eleni-Maria, Portelli, Stephanie and Ascher, David B. (2019). Exploring protein supersecondary structure through changes in protein folding, stability, and flexibility. Protein Supersecondary Structures: Methods and Protocols. (pp. 173-185) edited by Alexander E. Kister. New York, NY, United States: Springer. doi: 10.1007/978-1-4939-9161-7_9

A metabolic signature for NADSYN1-dependent congenital NAD deficiency disorder

Szot, Justin O., Cuny, Hartmut, Martin, Ella M.M.A., Sheng, Delicia Z., Iyer, Kavitha, Portelli, Stephanie, Nguyen, Vivien, Gereis, Jessica M., Alankarage, Dimuthu, Chitayat, David, Chong, Karen, Wentzensen, Ingrid M., Vincent-Delormé, Catherine, Lermine, Alban, Burkitt-Wright, Emma, Ji, Weizhen, Jeffries, Lauren, Pais, Lynn S., Tan, Tiong Y., Pitt, James, Wise, Cheryl A., Wright, Helen, Andrews, Israel D., Pruniski, Brianna, Grebe, Theresa A., Corsten-Janssen, Nicole, Bouman, Katelijne, Poulton, Cathryn, Prakash, Supraja ... Dunwoodie, Sally L. (2024). A metabolic signature for NADSYN1-dependent congenital NAD deficiency disorder. Journal of Clinical Investigation, 134 (4) 174824. doi: 10.1172/jci174824

Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges

Rodrigues, Carlos H. M., Portelli, Stephanie and Ascher, David B. (2024). Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges. Human Genetics, 1-9. doi: 10.1007/s00439-023-02623-4

Characterization on the oncogenic effect of the missense mutations of p53 via machine learning

Pan, Qisheng, Portelli, Stephanie, Nguyen, Thanh Binh and Ascher, David B (2023). Characterization on the oncogenic effect of the missense mutations of p53 via machine learning. Briefings in Bioinformatics, 25 (1) bbad428. doi: 10.1093/bib/bbad428

Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease

Serghini, Adam, Portelli, Stephanie, Troadec, Guillaume, Song, Catherine, Pan, Qisheng, Pires, Douglas E. V. and Ascher, David B. (2023). Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease. Human Molecular Genetics, 33 (3), 224-232. doi: 10.1093/hmg/ddad181

Identifying Innate Resistance Hotspots for SARS-CoV-2 Antivirals Using In Silico Protein Techniques

Portelli, Stephanie, Heaton, Ruby and Ascher, David B. (2023). Identifying Innate Resistance Hotspots for SARS-CoV-2 Antivirals Using In Silico Protein Techniques. Genes, 14 (9) 1699, 1699. doi: 10.3390/genes14091699

Identifying the molecular drivers of ALS-implicated missense mutations

Portelli, Stephanie, Albanaz, Amanda, Pires, Douglas Eduardo Valente and Ascher, David Benjamin (2022). Identifying the molecular drivers of ALS-implicated missense mutations. Journal of Medical Genetics, 60 (5) 108798, 1-7. doi: 10.1136/jmg-2022-108798

toxCSM: comprehensive prediction of small molecule toxicity profiles

de Sá, Alex G.C., Long, Yangyang, Portelli, Stephanie, Pires, Douglas E.V. and Ascher, David B. (2022). toxCSM: comprehensive prediction of small molecule toxicity profiles. Briefings in Bioinformatics, 23 (5) bbac337, 1-11. doi: 10.1093/bib/bbac337

Definition of the immune evasion-replication interface of rabies virus P protein

Zhan, Jingyu, Harrison, Angela R., Portelli, Stephanie, Nguyen, Thanh Binh, Kojima, Isshu, Zheng, Siqiong, Yan, Fei, Masatani, Tatsunori, Rawlinson, Stephen M., Sethi, Ashish, Ito, Naoto, Ascher, David B., Moseley, Gregory W. and Gooley, Paul R. (2021). Definition of the immune evasion-replication interface of rabies virus P protein. PLOS Pathogens, 17 (7) e1009729, 1-27. doi: 10.1371/journal.ppat.1009729

Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource

Portelli, Stephanie, Olshansky, Moshe, Rodrigues, Carlos H. M., D’Souza, Elston N., Myung, Yoochan, Silk, Michael, Alavi, Azadeh, Pires, Douglas E. V. and Ascher, David B. (2021). Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 53 (2), 254-254. doi: 10.1038/s41588-020-00775-x

Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase

Zhou, Yunzhuo, Portelli, Stephanie, Pat, Megan, Rodrigues, Carlos H.M., Nguyen, Thanh-Binh, Pires, Douglas E.V. and Ascher, David B. (2021). Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase. Computational and Structural Biotechnology Journal, 19, 5381-5391. doi: 10.1016/j.csbj.2021.09.016

ThermoMutDB: a thermodynamic database for missense mutations

Xavier, Joicymara S, Nguyen, Thanh-Binh, Karmarkar, Malancha, Portelli, Stephanie, Rezende, Pâmela M, Velloso, João P L, Ascher, David B and Pires, Douglas E V (2020). ThermoMutDB: a thermodynamic database for missense mutations. Nucleic Acids Research, 49 (D1), D475-D479. doi: 10.1093/nar/gkaa925

Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches

Portelli, Stephanie, Myung, Yoochan, Furnham, Nicholas, Vedithi, Sundeep Chaitanya, Pires, Douglas E. V. and Ascher, David B. (2020). Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches. Scientific Reports, 10 (1) 18120, 1-13. doi: 10.1038/s41598-020-74648-y

Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource

Portelli, Stephanie, Olshansky, Moshe, Rodrigues, Carlos H. M., D’Souza, Elston N., Myung, Yoochan, Silk, Michael, Alavi, Azadeh, Pires, Douglas E. V. and Ascher, David B. (2020). Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 52 (10), 999-1001. doi: 10.1038/s41588-020-0693-3

Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in

Vedithi, Sundeep Chaitanya, Rodrigues, Carlos H. M., Portelli, Stephanie, Skwark, Marcin J., Das, Madhusmita, Ascher, David B., Blundell, Tom L. and Malhotra, Sony (2020). Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in . Computational and Structural Biotechnology Journal, 18, 271-286. doi: 10.1016/j.csbj.2020.01.002

Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis

Portelli, Stephanie, Phelan, Jody E., Ascher, David B., Clark, Taane G. and Furnham, Nicholas (2018). Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. Scientific Reports, 8 (1) 15356. doi: 10.1038/s41598-018-33370-6