The University of Queensland

Using graph-based signatures to guide rational antibody engineering

Ascher, David B., Kaminskas, Lisa M., Myung, Yoochan and Pires, Douglas E. V. (2022). Using graph-based signatures to guide rational antibody engineering. Computer-aided antibody design. (pp. 375-397) New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-2609-2_21

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

Mutations in Glycosyltransferases and Glycosidases: Implications for Associated Diseases

Gu, Xiaotong, Kovacs, Aaron S., Myung, Yoochan and Ascher, David B. (2024). Mutations in Glycosyltransferases and Glycosidases: Implications for Associated Diseases. Biomolecules, 14 (4), 497. doi: 10.3390/biom14040497

Uncovering the molecular drivers of NHEJ DNA repair-implicated missense variants and their functional consequences

Al-Jarf, Raghad, Karmakar, Malancha, Myung, Yoochan and Ascher, David B. (2023). Uncovering the molecular drivers of NHEJ DNA repair-implicated missense variants and their functional consequences. Genes, 14 (10) 1890, 1-11. doi: 10.3390/genes14101890

Understanding the complementarity and plasticity of antibody–antigen interfaces

Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B (2023). Understanding the complementarity and plasticity of antibody–antigen interfaces. Bioinformatics, 39 (7) btad392, 1-7. doi: 10.1093/bioinformatics/btad392

VIVID: a web application for variant interpretation and visualisation in multidimensional analyses

Tichkule, Swapnil, Myung, Yoochan, Naung, Myo T., Ansell, Brendan R. E., Guy, Andrew J., Srivastava, Namrata, Mehra, Somya, Cacciò, Simone M, Mueller, Ivo, Barry, Alyssa E, van Oosterhout, Cock, Pope, Bernard, Ascher, David B and Jex, Aaron R (2022). VIVID: a web application for variant interpretation and visualisation in multidimensional analyses. Molecular Biology and Evolution, 39 (9) msac196. doi: 10.1093/molbev/msac196

Sequence grammar underlying the unfolding and phase separation of globular proteins

Ruff, Kiersten M., Choi, Yoon Hee, Cox, Dezerae, Ormsby, Angelique R., Myung, Yoochan, Ascher, David B., Radford, Sheena E., Pappu, Rohit V. and Hatters, Danny M. (2022). Sequence grammar underlying the unfolding and phase separation of globular proteins. Molecular Cell, 82 (17), 3193-3208.e8. doi: 10.1016/j.molcel.2022.06.024

mmCSM-NA: accurately predicting effects of single and multiple mutations on protein–nucleic acid binding affinity

Nguyen, Thanh Binh, Myung, Yoochan, de Sá, Alex G. C., Pires, Douglas E. V. and Ascher, David B. (2021). mmCSM-NA: accurately predicting effects of single and multiple mutations on protein–nucleic acid binding affinity. NAR Genomics and Bioinformatics, 3 (4) lqab109, lqab109. doi: 10.1093/nargab/lqab109

CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring function

Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2021). CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring function. Bioinformatics, 38 (4), 1141-1143. doi: 10.1093/bioinformatics/btab762

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

Lin, Heyu, Ascher, David B., Myung, Yoochan, Lamborg, Carl H., Hallam, Steven J., Gionfriddo, Caitlin M., Holt, Kathryn E. and Moreau, John W. (2021). Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. The ISME Journal, 15 (6), 1810-1825. doi: 10.1038/s41396-020-00889-4

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

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

mmCSM-AB: guiding rational antibody engineering through multiple point mutations

Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2020). mmCSM-AB: guiding rational antibody engineering through multiple point mutations. Nucleic Acids Research, 48 (W1), W125-W131. doi: 10.1093/nar/gkaa389

mCSM-AB2: guiding rational antibody design using graph-based signatures

Myung, Yoochan, Rodrigues, Carlos H. M., Ascher, David B. and Pires, Douglas E. V. (2020). mCSM-AB2: guiding rational antibody design using graph-based signatures. Bioinformatics, 36 (5), 1453-1459. doi: 10.1093/bioinformatics/btz779

Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

Seo, Myungwon, Shin, Hyun Kil, Myung, Yoochan, Hwang, Sungbo and No, Kyoung Tai (2020). Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development. Journal of Cheminformatics, 12 (1) 6, 1-17. doi: 10.1186/s13321-020-0410-3

mCSM-PPI2: predicting the effects of mutations on protein–protein interactions

Rodrigues, Carlos H. M., Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2019). mCSM-PPI2: predicting the effects of mutations on protein–protein interactions. Nucleic Acids Research, 47 (W1), W338-W344. doi: 10.1093/nar/gkz383