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

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

Prediction and optimization of pharmacokinetic and toxicity properties of the ligand

Pires, Douglas E. V., Kaminskas, Lisa M. and Ascher, David B. (2018). Prediction and optimization of pharmacokinetic and toxicity properties of the ligand. Computational Drug Discovery and Design. (pp. 271-284) New York, NY United States: Humana Press. doi: 10.1007/978-1-4939-7756-7_14

Protein-protein interactions: structures and druggability

Ascher, David B., Jubb, Harry C., Pires, Douglas E. V., Ochi, Takashi, Higueruelo, Alicia and Blundell, Tom L. (2015). Protein-protein interactions: structures and druggability. Multifaceted roles of crystallography in modern drug discovery. (pp. 141-163) Dordrecht, Netherlands: Springer Netherlands. doi: 10.1007/978-94-017-9719-1_12

epitope1D: accurate taxonomy-aware B-cell linear epitope prediction

da Silva, Bruna Moreira, Ascher, David B and Pires, Douglas E V (2023). epitope1D: accurate taxonomy-aware B-cell linear epitope prediction. Briefings in Bioinformatics, 24 (3). doi: 10.1093/bib/bbad114

Insights from Spatial Measures of Intolerance to Identifying Pathogenic Variants in Developmental and Epileptic Encephalopathies

Silk, Michael, de Sá, Alex, Olshansky, Moshe and Ascher, David B. (2023). Insights from Spatial Measures of Intolerance to Identifying Pathogenic Variants in Developmental and Epileptic Encephalopathies. International Journal of Molecular Sciences, 24 (6) 5114, 5114. doi: 10.3390/ijms24065114

CSM-Toxin: A Web-Server for Predicting Protein Toxicity

Morozov, Vladimir, Rodrigues, Carlos H. M. and Ascher, David B. (2023). CSM-Toxin: A Web-Server for Predicting Protein Toxicity. Pharmaceutics, 15 (2), 431. doi: 10.3390/pharmaceutics15020431

embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules

Aljarf, Raghad, Tang, Simon, Pires, Douglas E. V. and Ascher, David B. (2023). embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules. Journal of Chemical Information and Modeling, 63 (2), 432-441. doi: 10.1021/acs.jcim.2c00824

SARS-CoV-2 Africa dashboard for real-time COVID-19 information

Xavier, Joicymara S., Moir, Monika, Tegally, Houriiyah, Sitharam, Nikita, Abdool Karim, Wasim, San, James E., Linhares, Joana, Wilkinson, Eduan, Ascher, David B., Baxter, Cheryl, Pires, Douglas E. V. and de Oliveira, Tulio (2022). SARS-CoV-2 Africa dashboard for real-time COVID-19 information. Nature Microbiology, 8 (1), 1-4. doi: 10.1038/s41564-022-01276-9

A bias of Asparagine to Lysine mutations in SARS-CoV-2 outside the receptor binding domain affects protein flexibility

Boer, Jennifer C., Pan, Qisheng, Holien, Jessica K., Nguyen, Thanh-Binh, Ascher, David B. and Plebanski, Magdalena (2022). A bias of Asparagine to Lysine mutations in SARS-CoV-2 outside the receptor binding domain affects protein flexibility. Frontiers in Immunology, 13 954435. doi: 10.3389/fimmu.2022.954435

DockNet: high-throughput protein–protein interface contact prediction

Williams, Nathan P, Rodrigues, Carlos H M, Truong, Jia, Ascher, David B and Holien, Jessica K (2022). DockNet: high-throughput protein–protein interface contact prediction. Bioinformatics, 39 (1). doi: 10.1093/bioinformatics/btac797

A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanism

Parthasarathy, Shridhar, Ruggiero, Sarah McKeown, Gelot, Antoinette, Soardi, Fernanda C, Ribeiro, Bethânia F R, Pires, Douglas E V, Ascher, David B, Schmitt, Alain, Rambaud, Caroline, Represa, Alfonso, Xie, Hongbo M, Lusk, Laina, Wilmarth, Olivia, McDonnell, Pamela Pojomovsky, Juarez, Olivia A, Grace, Alexandra N, Buratti, Julien, Mignot, Cyril, Gras, Domitille, Nava, Caroline, Pierce, Samuel R, Keren, Boris, Kennedy, Benjamin C, Pena, Sergio D J, Helbig, Ingo and Cuddapah, Vishnu Anand (2022). A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanism. The American Journal of Human Genetics, 109 (12), 2253-2269. doi: 10.1016/j.ajhg.2022.11.002

A structural biology community assessment of AlphaFold2 applications

Akdel, Mehmet, Pires, Douglas E. V., Pardo, Eduard Porta, Jänes, Jürgen, Zalevsky, Arthur O., Mészáros, Bálint, Bryant, Patrick, Good, Lydia L., Laskowski, Roman A., Pozzati, Gabriele, Shenoy, Aditi, Zhu, Wensi, Kundrotas, Petras, Serra, Victoria Ruiz, Rodrigues, Carlos H. M., Dunham, Alistair S., Burke, David, Borkakoti, Neera, Velankar, Sameer, Frost, Adam, Basquin, Jérôme, Lindorff-Larsen, Kresten, Bateman, Alex, Kajava, Andrey V., Valencia, Alfonso, Ovchinnikov, Sergey, Durairaj, Janani, Ascher, David B., Thornton, Janet M. ... Beltrao, Pedro (2022). A structural biology community assessment of AlphaFold2 applications. Nature Structural & Molecular Biology, 29 (11), 1056-1067. doi: 10.1038/s41594-022-00849-w

<scp>kinCSM</scp> : Using graph‐based signatures to predict small molecule <scp>CDK2</scp> inhibitors

Zhou, Yunzhuo, Al‐Jarf, Raghad, Alavi, Azadeh, Nguyen, Thanh Binh, Rodrigues, Carlos H. M., Pires, Douglas E. V. and Ascher, David B. (2022). kinCSM : Using graph‐based signatures to predict small molecule CDK2 inhibitors. Protein Science, 31 (11) e4453, e4453. doi: 10.1002/pro.4453

cardioToxCSM: a web server for predicting cardiotoxicity of small molecules

Iftkhar, Saba, de Sá, Alex G. C., Velloso, João P. L., Aljarf, Raghad, Pires, Douglas E. V. and Ascher, David B. (2022). cardioToxCSM: a web server for predicting cardiotoxicity of small molecules. Journal of Chemical Information and Modeling, 62 (20), 4827-4836. doi: 10.1021/acs.jcim.2c00822

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

CSM‐peptides: A computational approach to rapid identification of therapeutic peptides

Rodrigues, Carlos H. M., Garg, Anjali, Keizer, David, Pires, Douglas E. V. and Ascher, David B. (2022). CSM‐peptides: A computational approach to rapid identification of therapeutic peptides. Protein Science, 31 (10) e4442, e4442. doi: 10.1002/pro.4442

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

GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms

Paiva, Vinícius A., Mendonça, Murillo V., Silveira, Sabrina A., Ascher, David B., Pires, Douglas E. V. and Izidoro, Sandro C. (2022). GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms. Briefings in Bioinformatics, 23 (5) bbac178, 1-9. doi: 10.1093/bib/bbac178

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

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

Use of cluster analysis to characterise aortic stenosis phenotypes with treatable and untreatable risk

Sen, J., Pires, D., de Sá, A., Ascher, D., Wahir, S. and Marwick, T. (2022). Use of cluster analysis to characterise aortic stenosis phenotypes with treatable and untreatable risk. Heart, Lung and Circulation, 31, S44-S45. doi: 10.1016/j.hlc.2022.06.016

HGDiscovery: an online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase

Karmakar, Malancha, Cicaloni, Vittoria, Rodrigues, Carlos H. M., Spiga, Ottavia, Santucci, Annalisa and Ascher, David B. (2022). HGDiscovery: an online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase. Current Research in Structural Biology, 4, 271-277. doi: 10.1016/j.crstbi.2022.08.001

CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning

Rodrigues, Carlos H. M. and Ascher, David B (2022). CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. Nucleic Acids Research, 50 (W1), W204-W209. doi: 10.1093/nar/gkac381

Evaluating hierarchical machine learning approaches to classify biological databases

Rezende, Pâmela M., Xavier, Joicymara S., Ascher, David B., Fernandes, Gabriel R. and Pires, Douglas E. V. (2022). Evaluating hierarchical machine learning approaches to classify biological databases. Briefings in Bioinformatics, 23 (4) bbac216, 1-14. doi: 10.1093/bib/bbac216

Structural landscapes of PPI interfaces

Rodrigues, Carlos H. M., Pires, Douglas E. V., Blundell, Tom L. and Ascher, David B. (2022). Structural landscapes of PPI interfaces. Briefings in Bioinformatics, 23 (4) bbac165, 1-10. doi: 10.1093/bib/bbac165

cropCSM: designing safe and potent herbicides with graph-based signatures

Pires, Douglas E V, Stubbs, Keith A, Mylne, Joshua S and Ascher, David B (2022). cropCSM: designing safe and potent herbicides with graph-based signatures. Briefings in Bioinformatics, 23 (2) bbac042. doi: 10.1093/bib/bbac042

Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures

Pan, Qisheng, Nguyen, Thanh Binh, Ascher, David B and Pires, Douglas E V (2022). Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. Briefings in Bioinformatics, 23 (2) bbac025. doi: 10.1093/bib/bbac025

Known allosteric proteins have central roles in genetic disease

Abrusán, György, Ascher, David B. and Inouye, Michael (2022). Known allosteric proteins have central roles in genetic disease. PLoS Computational Biology, 18 (2) e1009806, 1-28. doi: 10.1371/journal.pcbi.1009806

epitope3D: a machine learning method for conformational B-cell epitope prediction

da Silva, Bruna Moreira, Myung, YooChan, Ascher, David B. and Pires, Douglas E. V. (2022). epitope3D: a machine learning method for conformational B-cell epitope prediction. Briefings in Bioinformatics, 23 (1) bbab423, 1-8. doi: 10.1093/bib/bbab423

Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria

Sharma, Mahima, Lingford, James P., Petricevic, Marija, Snow, Alexander J. D., Zhang, Yunyang, Järvå, Michael A., Mui, Janice W.-Y., Scott, Nichollas E., Saunders, Eleanor C., Mao, Runyu, Epa, Ruwan, da Silva, Bruna M., Pires, Douglas E. V., Ascher, David B., McConville, Malcolm J., Davies, Gideon J., Williams, Spencer J. and Goddard-Borger, Ethan D. (2022). Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Proceedings of the National Academy of Sciences, 119 (4), e2116022119. doi: 10.1073/pnas.2116022119

CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function

Nguyen, Thanh Binh, Pires, Douglas E. V. and Ascher, David B. (2022). CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function. Briefings in Bioinformatics, 23 (1) bbab512, 1-8. doi: 10.1093/bib/bbab512

TSMDA: Target and symptom-based computational model for miRNA-disease-association prediction

Uthayopas, Korawich, de Sá, Alex G.C., Alavi, Azadeh, Pires, Douglas E.V. and Ascher, David B. (2021). TSMDA: Target and symptom-based computational model for miRNA-disease-association prediction. Molecular Therapy - Nucleic Acids, 26, 536-546. doi: 10.1016/j.omtn.2021.08.016

PdCSM-PPI: Using graph-based signatures to identify protein-protein interaction inhibitors

Rodrigues, Carlos H.M., Pires, Douglas E.V. and Ascher, David B. (2021). PdCSM-PPI: Using graph-based signatures to identify protein-protein interaction inhibitors. Journal of Chemical Information and Modeling, 61 (11), 5438-5445. doi: 10.1021/acs.jcim.1c01135

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

A novel deep intronic variant strongly associates with Alkaptonuria

Lai, Chien-Yi, Tsai, I-Jung, Chiu, Pao-Chin, Ascher, David B., Chien, Yin-Hsiu, Huang, Yu-Hsuan, Lin, Yi-Lin, Hwu, Wuh-Liang and Lee, Ni-Chung (2021). A novel deep intronic variant strongly associates with Alkaptonuria. npj Genomic Medicine, 6 (1) 89, 89. doi: 10.1038/s41525-021-00252-2

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. doi: 10.1371/journal.ppat.1009729

MTR3D: identifying regions within protein tertiary structures under purifying selection

Silk, Michael, Pires, Douglas E V, Rodrigues, Carlos H M, D’Souza, Elston N, Olshansky, Moshe, Thorne, Natalie and Ascher, David B (2021). MTR3D: identifying regions within protein tertiary structures under purifying selection. Nucleic Acids Research, 49 (W1), W438-W445. doi: 10.1093/nar/gkab428

pdCSM-cancer: using graph-based signatures to identify small molecules with anticancer properties

Al-Jarf, Raghad, de Sá, Alex G. C., Pires, Douglas E. V. and Ascher, David B. (2021). pdCSM-cancer: using graph-based signatures to identify small molecules with anticancer properties. Journal of Chemical Information and Modeling, 61 (7), 3314-3322. doi: 10.1021/acs.jcim.1c00168

mmCSM-PPI: predicting the effects of multiple point mutations on protein–protein interactions

Rodrigues, Carlos H. M., Pires, Douglas E. V. and Ascher, David B. (2021). mmCSM-PPI: predicting the effects of multiple point mutations on protein–protein interactions. Nucleic Acids Research, 49 (W1), W417-W424. doi: 10.1093/nar/gkab273

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

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

Unveiling six potent and highly selective antileishmanial agents via the open source compound collection ‘Pathogen Box’ against antimony-sensitive and -resistant Leishmania braziliensis

Souza Silva, Juliano A., Tunes, Luiza G., Coimbra, Roney S., Ascher, David B., Pires, Douglas E.V. and Monte-Neto, Rubens L. (2021). Unveiling six potent and highly selective antileishmanial agents via the open source compound collection ‘Pathogen Box’ against antimony-sensitive and -resistant Leishmania braziliensis. Biomedicine and Pharmacotherapy, 133 111049, 111049. doi: 10.1016/j.biopha.2020.111049

pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures

Velloso, João Paulo L., Ascher, David B. and Pires, Douglas E. V. (2021). pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures. Bioinformatics Advances, 1 (1), vbab031. doi: 10.1093/bioadv/vbab031

A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction

Hildebrand, Joanne M., Kauppi, Maria, Majewski, Ian J., Liu, Zikou, Cox, Allison J., Miyake, Sanae, Petrie, Emma J., Silk, Michael A., Li, Zhixiu, Tanzer, Maria C., Brumatti, Gabriela, Young, Samuel N., Hall, Cathrine, Garnish, Sarah E., Corbin, Jason, Stutz, Michael D., Di Rago, Ladina, Gangatirkar, Pradnya, Josefsson, Emma C., Rigbye, Kristin, Anderton, Holly, Rickard, James A., Tripaydonis, Anne, Sheridan, Julie, Scerri, Thomas S., Jackson, Victoria E., Czabotar, Peter E., Zhang, Jian-Guo, Varghese, Leila ... Silke, John (2020). A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction. Nature Communications, 11 (1) 3150, 3150. doi: 10.1038/s41467-020-16819-z

The impact of size and charge on the pulmonary pharmacokinetics and immunological response of the lungs to PLGA nanoparticles after intratracheal administration to rats

Haque, Shadabul, Pouton, Colin W., McIntosh, Michelle P., Ascher, David B, Keizer, David W, Whittaker, Michael R. and Kaminskas, Lisa M. (2020). The impact of size and charge on the pulmonary pharmacokinetics and immunological response of the lungs to PLGA nanoparticles after intratracheal administration to rats. Nanomedicine: Nanotechnology, Biology, and Medicine, 30 102291, 102291. doi: 10.1016/j.nano.2020.102291

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

DynaMut2 : Assessing changes in stability and flexibility upon single and multiple point missense mutations

Rodrigues, Carlos H.M., Pires, Douglas E.V. and Ascher, David B. (2020). DynaMut2 : Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Science, 30 (1), 60-69. doi: 10.1002/pro.3942

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

EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening

Pires, Douglas E V, Veloso, Wandré N P, Myung, YooChan, Rodrigues, Carlos H M, Silk, Michael, Rezende, Pâmela M, Silva, Francislon, Xavier, Joicymara S, Velloso, João P L, da Silveira, Carlos H and Ascher, David B (2020). EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening. Bioinformatics, 36 (14), 4200-4202. doi: 10.1093/bioinformatics/btaa480

mycoCSM: Using graph-based signatures to identify safe potent hits against Mycobacteria

Pires, Douglas E. V. and Ascher, David B. (2020). mycoCSM: Using graph-based signatures to identify safe potent hits against Mycobacteria. Journal of Chemical Information and Modeling, 60 (7), 3450-3456. doi: 10.1021/acs.jcim.0c00362

mCSM-membrane: predicting the effects of mutations on transmembrane proteins

Pires, Douglas E V, Rodrigues, Carlos H M and Ascher, David B (2020). mCSM-membrane: predicting the effects of mutations on transmembrane proteins. Nucleic Acids Research, 48 (W1), W147-W153. doi: 10.1093/nar/gkaa416

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

Structure guided prediction of Pyrazinamide resistance mutations in pncA

Karmakar, Malancha, Rodrigues, Carlos H. M., Horan, Kristy, Denholm, Justin T. and Ascher, David B. (2020). Structure guided prediction of Pyrazinamide resistance mutations in pncA. Scientific Reports, 10 (1) 1875, 1875. doi: 10.1038/s41598-020-58635-x

Widespread remodeling of proteome solubility in response to different protein homeostasis stresses

Sui, Xiaojing, Pires, Douglas E V, Ormsby, Angelique R, Cox, Dezerae, Nie, Shuai, Vecchi, Giulia, Vendruscolo, Michele, Ascher, David B, Reid, Gavin E and Hatters, Danny M (2020). Widespread remodeling of proteome solubility in response to different protein homeostasis stresses. Proceedings of the National Academy of Sciences of the United States of America, 117 (5), 2422-2431. doi: 10.1073/pnas.1912897117

Variant type is associated with disease characteristics in SDHB, SDHC and SDHD-linked phaeochromocytoma-paraganglioma

Bayley, Jean Pierre, Bausch, Birke, Rijken, Johannes Adriaan, van Hulsteijn, Leonie Theresia, Jansen, Jeroen C., Ascher, David, Pires, Douglas Eduardo Valente, Hes, Frederik J., Hensen, Erik F., Corssmit, Eleonora P. M., Devilee, Peter and Neumann, Hartmut P. H. (2020). Variant type is associated with disease characteristics in SDHB, SDHC and SDHD-linked phaeochromocytoma-paraganglioma. Journal of Medical Genetics, 57 (2), 96-103. doi: 10.1136/jmedgenet-2019-106214

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

Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH)

Trapero, Ana, Pacitto, Angela, Chan, Daniel Shiu-Hin, Abell, Chris, Blundell, Tom L., Ascher, David B. and Coyne, Anthony G. (2020). Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH). Bioorganic and Medicinal Chemistry Letters, 30 (2) 126792, 126792. doi: 10.1016/j.bmcl.2019.126792

Hyper transmission of Beijing lineage Mycobacterium tuberculosis: systematic review and meta-analysis

Karmakar, Malancha, Trauer, James M, Ascher, David B and Denholm, Justin T (2019). Hyper transmission of Beijing lineage Mycobacterium tuberculosis: systematic review and meta-analysis. The Journal of Infection, 79 (6), 572-581. doi: 10.1016/j.jinf.2019.09.016

dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction

Kaminskas, Lisa M., Pires, Douglas E. V. and Ascher, David B. (2019). dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction. Scientific Reports, 9 (1) 15465, 15465. doi: 10.1038/s41598-019-51789-3

Nedd8 hydrolysis by UCH proteases in Plasmodium parasites

Karpiyevich, Maryia, Adjalley, Sophie, Mol, Marco, Ascher, David B., Mason, Bethany, van der Heden van Noort, Gerbrand J., Laman, Heike, Ovaa, Huib, Lee, Marcus C. S. and Artavanis-Tsakonas, Katerina (2019). Nedd8 hydrolysis by UCH proteases in Plasmodium parasites. PLoS Pathogens, 15 (10), e1008086. doi: 10.1371/journal.ppat.1008086

ProCarbDB: a database of carbohydrate-binding proteins

Copoiu, Liviu, Torres, Pedro H M, Ascher, David B, Blundell, Tom L and Malhotra, Sony (2019). ProCarbDB: a database of carbohydrate-binding proteins. Nucleic Acids Research, 48 (D1), D368-D375. doi: 10.1093/nar/gkz860

A family of dual-activity glycosyltransferase-phosphorylases mediates mannogen turnover and virulence in Leishmania parasites

Sernee, M. Fleur, Ralton, Julie E., Nero, Tracy L., Sobala, Lukasz F., Kloehn, Joachim, Vieira-Lara, Marcel A., Cobbold, Simon A., Stanton, Lauren, Pires, Douglas E. V., Hanssen, Eric, Males, Alexandra, Ward, Tom, Bastidas, Laurence M., van der Peet, Phillip L., Parker, Michael W., Ascher, David B., Williams, Spencer J., Davies, Gideon J. and McConville, Malcolm J. (2019). A family of dual-activity glycosyltransferase-phosphorylases mediates mannogen turnover and virulence in Leishmania parasites. Cell Host and Microbe, 26 (3), 385-399.e9. doi: 10.1016/j.chom.2019.08.009

Synthesis and structure-activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH

Singh, Vinayak, Pacitto, Angela, Donini, Stefano, Ferraris, Davide M, Boros, Sándor, Illyés, Eszter, Szokol, Bálint, Rizzi, Menico, Blundell, Tom L, Ascher, David B, Pato, Janos and Mizrahi, Valerie (2019). Synthesis and structure-activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH. European Journal of Medicinal Chemistry, 174, 309-329. doi: 10.1016/j.ejmech.2019.04.027

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

MTR-Viewer: identifying regions within genes under purifying selection

Silk, Michael, Petrovski, Slavé and Ascher, David B (2019). MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Research, 47 (W1), W121-W126. doi: 10.1093/nar/gkz457

Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU

Ascher, David B, Spiga, Ottavia, Sekelska, Martina, Pires, Douglas E V, Bernini, Andrea, Tiezzi, Monica, Kralovicova, Jana, Borovska, Ivana, Soltysova, Andrea, Olsson, Birgitta, Galderisi, Silvia, Cicaloni, Vittoria, Ranganath, Lakshminarayan, Santucci, Annalisa and Zatkova, Andrea (2019). Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU. European Journal of Human Genetics : EJHG, 27 (6), 888-902. doi: 10.1038/s41431-019-0354-0

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE

Karmakar, Malancha, Rodrigues, Carlos H M, Holt, Kathryn E, Dunstan, Sarah J, Denholm, Justin and Ascher, David B (2019). Empirical ways to identify novel Bedaquiline resistance mutations in AtpE. PloS one, 14 (5) e0217169, e0217169. doi: 10.1371/journal.pone.0217169

Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations

Jatana, Nidhi, Ascher, David B., Pires, Douglas E.V., Gokhale, Rajesh S. and Thukral, Lipi (2019). Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations. Autophagy, 16 (2), 239-255. doi: 10.1080/15548627.2019.1606636

A 30 kDa polyethylene glycol-enfuvirtide complex enhances the exposure of enfuvirtide in lymphatic viral reservoirs in rats

Kaminskas, Lisa M., Williams, Charlotte C., Leong, Nathania J., Chan, Linda J., Butcher, Neville J., Feeney, Orlagh M., Porter, Christopher J.H., Tyssen, David, Tachedjian, Gilda and Ascher, David B. (2019). A 30 kDa polyethylene glycol-enfuvirtide complex enhances the exposure of enfuvirtide in lymphatic viral reservoirs in rats. European Journal of Pharmaceutics and Biopharmaceutics, 137, 218-226. doi: 10.1016/j.ejpb.2019.03.008

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

Structural and biochemical insights into the function and evolution of sulfoquinovosidases

Abayakoon, Palika, Jin, Yi, Lingford, James P., Petricevic, Marija, John, Alan, Ryan, Eileen, Wai-Ying Mui, Janice, Pires, Douglas E.V., Ascher, David B., Davies, Gideon J., Goddard-Borger, Ethan D. and Williams, Spencer J. (2018). Structural and biochemical insights into the function and evolution of sulfoquinovosidases. ACS Central Science, 4 (9), 1266-1273. doi: 10.1021/acscentsci.8b00453

Analysis of a novel pncA mutation for susceptibility to pyrazinamide therapy

Karmakar, Malancha, Globan, Maria, Fyfe, Janet A. M., Stinear, Timothy P., Johnson, Paul D. R., Holmes, Natasha E., Denholm, Justin T. and Ascher, David B. (2018). Analysis of a novel pncA mutation for susceptibility to pyrazinamide therapy. American Journal of Respiratory and Critical Care Medicine, 198 (4), 541-544. doi: 10.1164/rccm.201712-2572le

Kinact: a computational approach for predicting activating missense mutations in protein kinases

Rodrigues, Carlos H.M., Ascher, David B. and Pires, Douglas E.V. (2018). Kinact: a computational approach for predicting activating missense mutations in protein kinases. Nucleic Acids Research, 46 (W1), W127-W132. doi: 10.1093/nar/gky375

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

Holt, Kathryn E, McAdam, Paul, Thai, Phan Vuong Khac, Thuong, Nguyen Thuy Thuong, Ha, Dang Thi Minh, Lan, Nguyen Ngoc, Lan, Nguyen Huu, Nhu, Nguyen Thi Quynh, Hai, Hoang Thanh, Ha, Vu Thi Ngoc, Thwaites, Guy, Edwards, David J, Nath, Artika P, Pham, Kym, Ascher, David B, Farrar, Jeremy, Khor, Chiea Chuen, Teo, Yik Ying, Inouye, Michael, Caws, Maxine and Dunstan, Sarah J (2018). Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nature Genetics, 50 (6), 849-856. doi: 10.1038/s41588-018-0117-9

Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation

Hnízda, Aleš, Fábry, Milan, Moriyama, Takaya, Pachl, Petr, Kugler, Michael, Brinsa, Vítězslav, Ascher, David B, Carroll, William L, Novák, Petr, Žaliová, Markéta, Trka, Jan, Řezáčová, Pavlína, Yang, Jun J and Veverka, Václav (2018). Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation. Leukemia, 32 (6), 1393-1403. doi: 10.1038/s41375-018-0073-5

Tumour risks and genotype-phenotype correlations associated with germline variants in succinate dehydrogenase subunit genes , and

Andrews, Katrina A, Ascher, David B, Pires, Douglas Eduardo Valente, Barnes, Daniel R, Vialard, Lindsey, Casey, Ruth T, Bradshaw, Nicola, Adlard, Julian, Aylwin, Simon, Brennan, Paul, Brewer, Carole, Cole, Trevor, Cook, Jackie A, Davidson, Rosemarie, Donaldson, Alan, Fryer, Alan, Greenhalgh, Lynn, Hodgson, Shirley V, Irving, Richard, Lalloo, Fiona, McConachie, Michelle, McConnell, Vivienne P M, Morrison, Patrick J, Murday, Victoria, Park, Soo-Mi, Simpson, Helen L, Snape, Katie, Stewart, Susan, Tomkins, Susan E ... Maher, Eamonn R (2018). Tumour risks and genotype-phenotype correlations associated with germline variants in succinate dehydrogenase subunit genes , and . Journal of Medical Genetics, 55 (6), 384-394. doi: 10.1136/jmedgenet-2017-105127

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

Rodrigues, Carlos H.M., Pires, Douglas E.V. and Ascher, David B. (2018). DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. Nucleic Acids Research, 46 (W1), W350-W355. doi: 10.1093/nar/gky300

Fragment-based approach to targeting inosine-5'-monophosphate dehydrogenase (IMPDH) from Mycobacterium tuberculosis

Trapero, Ana, Pacitto, Angela, Singh, Vinayak, Sabbah, Mohamad, Coyne, Anthony G, Mizrahi, Valerie, Blundell, Tom L, Ascher, David B and Abell, Chris (2018). Fragment-based approach to targeting inosine-5'-monophosphate dehydrogenase (IMPDH) from Mycobacterium tuberculosis. Journal of Medicinal Chemistry, 61 (7), 2806-2822. doi: 10.1021/acs.jmedchem.7b01622

Structural implications of mutations conferring rifampin resistance in Mycobacterium leprae

Vedithi, Sundeep Chaitanya, Malhotra, Sony, Das, Madhusmita, Daniel, Sheela, Kishore, Nanda, George, Anuja, Arumugam, Shantha, Rajan, Lakshmi, Ebenezer, Mannam, Ascher, David B, Arnold, Eddy and Blundell, Tom L (2018). Structural implications of mutations conferring rifampin resistance in Mycobacterium leprae. Scientific Reports, 8 (1) 5016. doi: 10.1038/s41598-018-23423-1

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection

Hawkey, Jane, Ascher, David B, Judd, Louise M, Wick, Ryan R, Kostoulias, Xenia, Cleland, Heather, Spelman, Denis W, Padiglione, Alex, Peleg, Anton Y and Holt, Kathryn E (2018). Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection. Microbial Genomics, 4 (3). doi: 10.1099/mgen.0.000165

A computational approach from gene to structure analysis of the human ABCA4 transporter involved in genetic retinal diseases

Trezza, Alfonso, Bernini, Andrea, Langella, Andrea, Ascher, David B, Pires, Douglas E V, Sodi, Andrea, Passerini, Ilaria, Pelo, Elisabetta, Rizzo, Stanislao, Niccolai, Neri and Spiga, Ottavia (2017). A computational approach from gene to structure analysis of the human ABCA4 transporter involved in genetic retinal diseases. Investigative Ophthalmology and Visual Science, 58 (12), 5320-5328. doi: 10.1167/iovs.17-22158

Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation

Traynelis, Joshua, Silk, Michael, Wang, Quanli, Berkovic, Samuel F, Liu, Liping, Ascher, David B, Balding, David J and Petrovski, Slavé (2017). Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation. Genome Research, 27 (10), 1715-1729. doi: 10.1101/gr.226589.117

Mutations at protein-protein interfaces: small changes over big surfaces have large impacts on human health

Jubb, Harry C, Pandurangan, Arun P, Turner, Meghan A, Ochoa-Montaño, Bernardo, Blundell, Tom L and Ascher, David B (2017). Mutations at protein-protein interfaces: small changes over big surfaces have large impacts on human health. Progress in Biophysics and Molecular Biology, 128, 3-13. doi: 10.1016/j.pbiomolbio.2016.10.002

Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design

Albanaz, Amanda T S, Rodrigues, Carlos H M, Pires, Douglas E V and Ascher, David B (2017). Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design. Expert Opinion on Drug Discovery, 12 (6), 553-563. doi: 10.1080/17460441.2017.1322579

SDM: a server for predicting effects of mutations on protein stability

Pandurangan, Arun Prasad, Ochoa-Montaño, Bernardo, Ascher, David B. and Blundell, Tom L. (2017). SDM: a server for predicting effects of mutations on protein stability. Nucleic Acids Research, 45 (W1), W229-W235. doi: 10.1093/nar/gkx439

DNA-PKcs, allostery, and DNA double-strand break repair: defining the structure and setting the stage

Chirgadze, Dimitri Y, Ascher, David B, Blundell, Tom L and Sibanda, Bancinyane L (2017). DNA-PKcs, allostery, and DNA double-strand break repair: defining the structure and setting the stage. Methods in Enzymology, 592, 145-157. doi: 10.1016/bs.mie.2017.04.001

Dimeric but not monomeric α-lactalbumin potentiates apoptosis by up regulation of ATF3 and reduction of histone deacetylase activity in primary and immortalised cells

Sharp, Julie A, Brennan, Amelia J, Polekhina, Galina, Ascher, David B, Lefevre, Christophe and Nicholas, Kevin R (2017). Dimeric but not monomeric α-lactalbumin potentiates apoptosis by up regulation of ATF3 and reduction of histone deacetylase activity in primary and immortalised cells. Cellular Signalling, 33, 86-97. doi: 10.1016/j.cellsig.2017.02.007

Huntingtin inclusions trigger cellular quiescence, deactivate apoptosis, and lead to delayed necrosis

Ramdzan, Yasmin M., Trubetskov, Mikhail M., Ormsby, Angelique R., Newcombe, Estella A., Sui, Xiaojing, Tobin, Mark J., Bongiovanni, Marie N., Gras, Sally L., Dewson, Grant, Miller, Jason M. L., Finkbeiner, Steven, Moily, Nagaraj S., Niclis, Jonathan, Parish, Clare L., Purcell, Anthony W., Baker, Michael J., Wilce, Jacqueline A., Waris, Saboora, Stojanovski, Diana, Bocking, Till, Ang, Ching-Seng, Ascher, David B., Reid, Gavin E. and Hatters, Danny M. (2017). Huntingtin inclusions trigger cellular quiescence, deactivate apoptosis, and lead to delayed necrosis. Cell Reports, 19 (5), 919-927. doi: 10.1016/j.celrep.2017.04.029

SDHA related tumorigenesis: a new case series and literature review for variant interpretation and pathogenicity

Casey, Ruth T, Ascher, David B, Rattenberry, Eleanor, Izatt, Louise, Andrews, Katrina A, Simpson, Helen L, Challis, Benjamen, Park, Soo-Mi, Bulusu, Venkata R, Lalloo, Fiona, Pires, Douglas E V, West, Hannah, Clark, Graeme R, Smith, Philip S, Whitworth, James, Papathomas, Thomas G, Taniere, Phillipe, Savisaar, Rosina, Hurst, Laurence D, Woodward, Emma R and Maher, Eamonn R (2017). SDHA related tumorigenesis: a new case series and literature review for variant interpretation and pathogenicity. Molecular Genetics and Genomic Medicine, 5 (3), 237-250. doi: 10.1002/mgg3.279

Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance

Pandurangan, Arun Prasad, Ascher, David B., Thomas, Sherine E. and Blundell, Tom L. (2017). Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance. Biochemical Society Transactions, 45 (2), 303-311. doi: 10.1042/BST20160422

mCSM–NA: predicting the effects of mutations on protein–nucleic acids interactions

Pires, Douglas E.V. and Ascher, David B. (2017). mCSM–NA: predicting the effects of mutations on protein–nucleic acids interactions. Nucleic Acids Research, 45 (W1), W241-W246. doi: 10.1093/nar/gkx236

Familial germline mutation defines a new human cohesinopathy

Soardi, Fernanda C, Machado-Silva, Alice, Linhares, Natália D, Zheng, Ge, Qu, Qianhui, Pena, Heloísa B, Martins, Thaís M M, Vieira, Helaine G S, Pereira, Núbia B, Melo-Minardi, Raquel C, Gomes, Carolina C, Gomez, Ricardo S, Gomes, Dawidson A, Pires, Douglas E V, Ascher, David B, Yu, Hongtao and Pena, Sérgio D J (2017). Familial germline mutation defines a new human cohesinopathy. NPJ Genomic Medicine, 2 (1) 7. doi: 10.1038/s41525-017-0009-4

Arpeggio: a web server for calculating and visualising interatomic interactions in protein structures

Jubb, Harry C, Higueruelo, Alicia P, Ochoa-Montaño, Bernardo, Pitt, Will R, Ascher, David B and Blundell, Tom L (2017). Arpeggio: a web server for calculating and visualising interatomic interactions in protein structures. Journal of Molecular Biology, 429 (3), 365-371. doi: 10.1016/j.jmb.2016.12.004

DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair

Sibanda, Bancinyane L, Chirgadze, Dimitri Y, Ascher, David B and Blundell, Tom L (2017). DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair. Science, 355 (6324), 520-524. doi: 10.1126/science.aak9654

Essential but not vulnerable: indazole sulfonamides targeting inosine monophosphate dehydrogenase as potential leads against Mycobacterium tuberculosis

Park, Yumi, Pacitto, Angela, Bayliss, Tracy, Cleghorn, Laura A T, Wang, Zhe, Hartman, Travis, Arora, Kriti, Ioerger, Thomas R, Sacchettini, Jim, Rizzi, Menico, Donini, Stefano, Blundell, Tom L, Ascher, David B, Rhee, Kyu, Breda, Ardala, Zhou, Nian, Dartois, Veronique, Jonnala, Surendranadha Reddy, Via, Laura E, Mizrahi, Valerie, Epemolu, Ola, Stojanovski, Laste, Simeons, Fred, Osuna-Cabello, Maria, Ellis, Lucy, MacKenzie, Claire J, Smith, Alasdair R C, Davis, Susan H, Murugesan, Dinakaran ... Boshoff, Helena I (2017). Essential but not vulnerable: indazole sulfonamides targeting inosine monophosphate dehydrogenase as potential leads against Mycobacterium tuberculosis. ACS Infectious Diseases, 3 (1), 18-33. doi: 10.1021/acsinfecdis.6b00103

The inosine monophosphate dehydrogenase, GuaB2, is a vulnerable new bactericidal drug target for tuberculosis

Singh, Vinayak, Donini, Stefano, Pacitto, Angela, Sala, Claudia, Hartkoorn, Ruben C., Dhar, Neeraj, Keri, Gyorgy, Ascher, David B., Mondésert, Guillaume, Vocat, Anthony, Lupien, Andréanne, Sommer, Raphael, Vermet, Hélène, Lagrange, Sophie, Buechler, Joe, Warner, Digby F., McKinney, John D., Pato, Janos, Cole, Stewart T., Blundell, Tom L., Rizzi, Menico and Mizrahi, Valerie (2017). The inosine monophosphate dehydrogenase, GuaB2, is a vulnerable new bactericidal drug target for tuberculosis. ACS Infectious Diseases, 3 (1), 5-17. doi: 10.1021/acsinfecdis.6b00102

Achieving selectivity in space and time with DNA double-strand-break response and repair: molecular stages and scaffolds come with strings attached

Liang, S., Esswein, S. R., Ochi, T., Wu, Q., Ascher, D. B., Chirgadze, D., Sibanda, B. L. and Blundell, T. L. (2017). Achieving selectivity in space and time with DNA double-strand-break response and repair: molecular stages and scaffolds come with strings attached. Structural Chemistry, 28 (1), 161-171. doi: 10.1007/s11224-016-0841-7

The presence, persistence and functional properties of Plasmodium vivax duffy binding protein II antibodies are influenced by HLA class II allelic variants

Kano, Flora S, Souza-Silva, Flávia A, Torres, Leticia M, Lima, Barbara A S, Sousa, Taís N, Alves, Jéssica R S, Rocha, Roberto S, Fontes, Cor J F, Sanchez, Bruno A M, Adams, John H, Brito, Cristiana F A, Pires, Douglas E V, Ascher, David B, Sell, Ana Maria and Carvalho, Luzia H (2016). The presence, persistence and functional properties of Plasmodium vivax duffy binding protein II antibodies are influenced by HLA class II allelic variants. PLoS Neglected Tropical Diseases, 10 (12) e0005177. doi: 10.1371/journal.pntd.0005177

Ubiquitin-dependent modification of skeletal muscle by the parasitic nematode, Trichinella spiralis

White, Rhiannon R, Ponsford, Amy H, Weekes, Michael P, Rodrigues, Rachel B, Ascher, David B, Mol, Marco, Selkirk, Murray E, Gygi, Steven P, Sanderson, Christopher M and Artavanis-Tsakonas, Katerina (2016). Ubiquitin-dependent modification of skeletal muscle by the parasitic nematode, Trichinella spiralis. PLoS Pathogens, 12 (11) e1005977, e1005977. doi: 10.1371/journal.ppat.1005977

Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins

Coelho, Miguel B, Ascher, David B, Gooding, Clare, Lang, Emma, Maude, Hannah, Turner, David, Llorian, Miriam, Pires, Douglas E V, Attig, Jan and Smith, Christopher W J (2016). Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins. Biochemical Society Transactions, 44 (4), 1058-1065. doi: 10.1042/BST20160080

Variation in human cytochrome P-450 drug-metabolism genes: a gateway to the understanding of Plasmodium vivax relapses

Silvino, Ana Carolina Rios, Costa, Gabriel Luiz, Araújo, Flávia Carolina Faustino de, Ascher, David Benjamin, Pires, Douglas Eduardo Valente, Fontes, Cor Jesus Fernandes, Carvalho, Luzia Helena, Brito, Cristiana Ferreira Alves de and Sousa, Tais Nobrega (2016). Variation in human cytochrome P-450 drug-metabolism genes: a gateway to the understanding of Plasmodium vivax relapses. PLoS One, 11 (7), e0160172. doi: 10.1371/journal.pone.0160172

CSM-lig: a web server for assessing and comparing protein-small molecule affinities

Pires, Douglas E. V. and Ascher, David B (2016). CSM-lig: a web server for assessing and comparing protein-small molecule affinities. Nucleic Acids Research, 44 (W1), W557-W561. doi: 10.1093/nar/gkw390

mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures

Pires, Douglas E. V. and Ascher, David B. (2016). mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures. Nucleic Acids Research, 44 (W1), W469-W473. doi: 10.1093/nar/gkw458

mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance

Pires, Douglas E. V., Blundell, Tom L. and Ascher, David B. (2016). mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance. Scientific Reports, 6 (1) 29575, 29575. doi: 10.1038/srep29575

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

Phelan, Jody, Coll, Francesc, McNerney, Ruth, Ascher, David B., Pires, Douglas E. V., Furnham, Nick, Coeck, Nele, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ramsay, Andrew, Campino, Susana, Hibberd, Martin L., Pain, Arnab, Rigouts, Leen and Clark, Taane G. (2016). Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC Medicine, 14 (1) 31, 31. doi: 10.1186/s12916-016-0575-9

Conjugation of 10 kDa Linear PEG onto Trastuzumab Fab′ Is Sufficient to Significantly Enhance Lymphatic Exposure while Preserving in Vitro Biological Activity

Chan, Linda J., Ascher, David B., Yadav, Rajbharan, Bulitta, Jürgen B., Williams, Charlotte C., Porter, Christopher J. H., Landersdorfer, Cornelia B. and Kaminskas, Lisa M. (2016). Conjugation of 10 kDa Linear PEG onto Trastuzumab Fab′ Is Sufficient to Significantly Enhance Lymphatic Exposure while Preserving in Vitro Biological Activity. Molecular Pharmaceutics, 13 (4), 1229-1241. doi: 10.1021/acs.molpharmaceut.5b00749

Tumour risks and genotype–phenotype–proteotype analysis of patients with germline mutations in the succinate dehydrogenase subunit genes SDHB, SDHC, and SDHD

Andrews, Katrina A, Vialard, Lindsey, Ascher, David B, Pires, Douglas E V, Bradshaw, Nicola, Cole, Trevor, Cook, Jackie, Irving, Richard, Kumar, Ajith, Lalloo, Fiona, Izatt, Louise, Goudie, David, Woodward, Emma R and Maher, Eamonn R (2016). Tumour risks and genotype–phenotype–proteotype analysis of patients with germline mutations in the succinate dehydrogenase subunit genes SDHB, SDHC, and SDHD. The Lancet, 387, S19-S19. doi: 10.1016/s0140-6736(16)00406-2

In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity

Pires, Douglas E. V., Chen, Jing, Blundell, Tom L. and Ascher, David B. (2016). In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. Scientific Reports, 6 (1) 19848. doi: 10.1038/srep19848

Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on 'black bone disease' in Italy

Nemethova, Martina, Radvanszky, Jan, Kadasi, Ludevit, Ascher, David B., Pires, Douglas E. V., Blundell, Tom L., Porfirio, Berardino, Mannoni, Alessandro, Santucci, Annalisa, Milucci, Lia, Sestini, Silvia, Biolcati, Gianfranco, Sorge, Fiammetta, Aurizi, Caterina, Aquaron, Robert, Alsbou, Mohammed, Lourenço, Charles Marques, Ramadevi, Kanakasabapathi, Ranganath, Lakshminarayan R., Gallagher, James A., van Kan, Christa, Hall, Anthony K., Olsson, Birgitta, Sireau, Nicolas, Ayoob, Hana, Timmis, Oliver G., Sang, Kim-Hanh Le Quan, Genovese, Federica, Imrich, Richard ... Zatkova, Andrea (2016). Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on 'black bone disease' in Italy. European Journal of Human Genetics, 24 (1), 66-72. doi: 10.1038/ejhg.2015.60

PEGylated interferon displays differences in plasma clearance and bioavailability between male and female mice and between female immunocompetent C57Bl/6J and athymic nude mice

Landersdorfer, Cornelia B., Caliph, Suzanne M., Shackleford, David M., Ascher, David B. and Kaminskas, Lisa M. (2015). PEGylated interferon displays differences in plasma clearance and bioavailability between male and female mice and between female immunocompetent C57Bl/6J and athymic nude mice. Journal of Pharmaceutical Sciences, 104 (5), 1848-1855. doi: 10.1002/jps.24412

Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein

Pacitto, Angela, Ascher, David B, Wong, Louise H, Blaszczyk, Beata K, Nookala, Ravi K, Zhang, Nianshu, Dokudovskaya, Svetlana, Levine, Tim P and Blundell, Tom L (2015). Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein. Open Biology, 5 (12) 150174. doi: 10.1098/rsob.150174

Exploring the chemical space of the lysine-binding pocket of the first kringle domain of hepatocyte growth factor/scatter factor (HGF/SF) yields a new class of inhibitors of HGF/SF-MET binding

Sigurdardottir, A G, Winter, A, Sobkowicz, A, Fragai, M, Chirgadze, D, Ascher, D B, Blundell, T L and Gherardi, E (2015). Exploring the chemical space of the lysine-binding pocket of the first kringle domain of hepatocyte growth factor/scatter factor (HGF/SF) yields a new class of inhibitors of HGF/SF-MET binding. Chemical Science, 6 (11), 6147-6157. doi: 10.1039/c5sc02155c

Flexibility and small pockets at protein-protein interfaces: new insights into druggability

Jubb, Harry, Blundell, Tom L. and Ascher, David B. (2015). Flexibility and small pockets at protein-protein interfaces: new insights into druggability. Progress in Biophysics and Molecular Biology, 119 (1), 2-9. doi: 10.1016/j.pbiomolbio.2015.01.009

Achieving high signal-to-noise in cell regulatory systems: spatial organization of multiprotein transmembrane assemblies of FGFR and MET receptors

Blaszczyk, Michal, Harmer, Nicholas J., Chirgadze, Dimitri Y., Ascher, David B. and Blundell, Tom L. (2015). Achieving high signal-to-noise in cell regulatory systems: spatial organization of multiprotein transmembrane assemblies of FGFR and MET receptors. Progress in Biophysics and Molecular Biology, 118 (3), 103-11. doi: 10.1016/j.pbiomolbio.2015.04.007

Germline mutations in the CDKN2B tumor suppressor gene predispose to renal cell carcinoma

Jafri, Mariam, Wake, Naomi C, Ascher, David B, Pires, Douglas E V, Gentle, Dean, Morris, Mark R, Rattenberry, Eleanor, Simpson, Michael A, Trembath, Richard C, Weber, Astrid, Woodward, Emma R, Donaldson, Alan, Blundell, Tom L, Latif, Farida and Maher, Eamonn R (2015). Germline mutations in the CDKN2B tumor suppressor gene predispose to renal cell carcinoma. Cancer Discovery, 5 (7), 723-729. doi: 10.1158/2159-8290.CD-14-1096

pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures

Pires, Douglas E V, Blundell, Tom L and Ascher, David B (2015). pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58 (9), 4066-72. doi: 10.1021/acs.jmedchem.5b00104

Analysis of HGD gene mutations in patients with Alkaptonuria from the United Kingdom: identification of novel mutations

Usher, Jeannette L, Ascher, David B, Pires, Douglas E V, Milan, Anna M, Blundell, Tom L and Ranganath, Lakshminarayan R (2015). Analysis of HGD gene mutations in patients with Alkaptonuria from the United Kingdom: identification of novel mutations. JIMD Reports, 24, 3-11. doi: 10.1007/8904_2014_380

Methotrexate-conjugated PEGylated dendrimers show differential patterns of deposition and activity in tumor-burdened lymph nodes after intravenous and subcutaneous administration in rats

Kaminskas, Lisa M., McLeod, Victoria M., Ascher, David B., Ryan, Gemma M., Jones, Seth, Haynes, John M., Trevaskis, Natalie L., Chan, Linda J., Sloan, Erica K., Finnin, Benjamin A., Williamson, Mark, Velkov, Tony, Williams, Elizabeth D., Kelly, Brian D., Owen, David J. and Porter, Christopher J. H. (2015). Methotrexate-conjugated PEGylated dendrimers show differential patterns of deposition and activity in tumor-burdened lymph nodes after intravenous and subcutaneous administration in rats. Molecular Pharmaceutics, 12 (2), 432-443. doi: 10.1021/mp500531e

PEGylation does not significantly change the initial intravenous or subcutaneous pharmacokinetics or lymphatic exposure of trastuzumab in rats but increases plasma clearance after subcutaneous administration

Chan, Linda J., Bulitta, Jürgen B., Ascher, David B., Haynes, John Michael, McLeod, Victoria M., Porter, Christopher J. H., Williams, Charlotte C. and Kaminskas, Lisa M. (2015). PEGylation does not significantly change the initial intravenous or subcutaneous pharmacokinetics or lymphatic exposure of trastuzumab in rats but increases plasma clearance after subcutaneous administration. Molecular Pharmaceutics, 12 (3), 794-809. doi: 10.1021/mp5006189

Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides

Hermans, Stefan J, Ascher, David B, Hancock, Nancy C, Holien, Jessica K, Michell, Belinda J, Chai, Siew Yeen, Morton, Craig J and Parker, Michael W (2015). Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides. Protein Science, 24 (2), 190-199. doi: 10.1002/pro.2604

Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes

Pires, Douglas E V, Blundell, Tom L and Ascher, David B (2015). Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. Nucleic Acids Research, 43, D387-D391. doi: 10.1093/nar/gku966

Practical lessons in murine thoracic lymph duct cannulations: Observations in female and male mice across four different strains that impact on cannulatability

Caliph, Suzanne M., Shackleford, David M., Ascher, David B. and Kaminskas, Lisa M. (2014). Practical lessons in murine thoracic lymph duct cannulations: Observations in female and male mice across four different strains that impact on cannulatability. Journal of Pharmaceutical Sciences, 104 (3), 1207-1209. doi: 10.1002/jps.24312

Anti-Aβ antibody target engagement: a response to Siemers et al.

Watt, Andrew D, Crespi, Gabriela A N, Down, Russell A, Ascher, David B, Gunn, Adam, Perez, Keyla A, McLean, Catriona A, Villemagne, Victor L, Parker, Michael W, Barnham, Kevin J and Miles, Luke A (2014). Anti-Aβ antibody target engagement: a response to Siemers et al.. Acta Neuropathologica, 128 (4), 611-4. doi: 10.1007/s00401-014-1333-8

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

Pires, Douglas E. V., Ascher, David B. and Blundell, Tom L. (2014). DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Research, 42 (Web Server issue), W314-W319. doi: 10.1093/nar/gku411

Do current therapeutic anti-Aβ antibodies for Alzheimer's disease engage the target?

Watt, Andrew D, Crespi, Gabriela A N, Down, Russell A, Ascher, David B, Gunn, Adam, Perez, Keyla A, McLean, Catriona A, Villemagne, Victor L, Parker, Michael W, Barnham, Kevin J and Miles, Luke A (2014). Do current therapeutic anti-Aβ antibodies for Alzheimer's disease engage the target?. Acta Neuropathologica, 127 (6), 803-810. doi: 10.1007/s00401-014-1290-2

Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA

Ascher, David B., Wielens, Jerome, Nero, Tracy L., Doughty, Larissa, Morton, Craig J. and Parker, Michael W. (2014). Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA. Scientific Reports, 4 (1) 4765. doi: 10.1038/srep04765

Crystallization and preliminary X-ray diffraction analysis of the Fab portion of the Alzheimer's disease immunotherapy candidate bapineuzumab complexed with amyloid-β

Crespi, Gabriela A N, Ascher, David B, Parker, Michael W and Miles, Luke A (2014). Crystallization and preliminary X-ray diffraction analysis of the Fab portion of the Alzheimer's disease immunotherapy candidate bapineuzumab complexed with amyloid-β. Acta Crystallographica. Section F, Structural Biology Communications, 70 (Pt 3), 374-7. doi: 10.1107/S2053230X14001642

Structural studies of Streptococcus pyogenes streptolysin O provide insights into the early steps of membrane penetration

Feil, Susanne C, Ascher, David B, Kuiper, Michael J, Tweten, Rodney K and Parker, Michael W (2014). Structural studies of Streptococcus pyogenes streptolysin O provide insights into the early steps of membrane penetration. Journal of Molecular Biology, 426 (4), 785-792. doi: 10.1016/j.jmb.2013.11.020

mCSM: predicting the effects of mutations in proteins using graph-based signatures

Pires, Douglas E V, Ascher, David B and Blundell, Tom L (2014). mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics, 30 (3), 335-42. doi: 10.1093/bioinformatics/btt691

PEGylation of interferon α2 improves lymphatic exposure after subcutaneous and intravenous administration and improves antitumour efficacy against lymphatic breast cancer metastases

Kaminskas, Lisa M., Ascher, David B., McLeod, Victoria M., Herold, Marco J., Le, Caroline P., Sloan, Erica K. and Porter, Christopher J. H. (2013). PEGylation of interferon α2 improves lymphatic exposure after subcutaneous and intravenous administration and improves antitumour efficacy against lymphatic breast cancer metastases. Journal of Controlled Release, 168 (2), 200-208. doi: 10.1016/j.jconrel.2013.03.006

Structure of the N-terminal domain of human thioredoxin-interacting protein

Polekhina, Galina, Ascher, David Benjamin, Kok, Shie Foong, Beckham, Simone, Wilce, Matthew and Waltham, Mark (2013). Structure of the N-terminal domain of human thioredoxin-interacting protein. Acta Crystallographica. Section D: Structural Biology, 69 (Pt 3), 333-344. doi: 10.1107/S0907444912047099

Structural approaches to probing metal interaction with proteins

Parker, Lorien J, Ascher, David B, Gao, Chen, Miles, Luke A, Harris, Hugh H and Parker, Michael W (2012). Structural approaches to probing metal interaction with proteins. Journal of Inorganic Biochemistry, 115, 138-47. doi: 10.1016/j.jinorgbio.2012.02.015

Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2

Ascher, David B, Polekhina, Galina and Parker, Michael W (2012). Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2. Acta Crystallographica. Section F: Structural Biology Communications, 68 (Pt 4), 468-71. doi: 10.1107/S1744309112006963

Crystallization and preliminary X-ray analysis of the N-terminal domain of human thioredoxin-interacting protein

Polekhina, Galina, Ascher, David Benjamin, Kok, Shie Foong and Waltham, Mark (2011). Crystallization and preliminary X-ray analysis of the N-terminal domain of human thioredoxin-interacting protein. Acta Crystallographica. Section F: Structural Biology Communications, 67 (Pt 5), 613-617. doi: 10.1107/S1744309111010347

Regulation of insulin-regulated membrane aminopeptidase activity by its C-terminal domain

Ascher, David B, Cromer, Brett A, Morton, Craig J, Volitakis, Irene, Cherny, Robert A, Albiston, Anthony L, Chai, Siew Yeen and Parker, Michael W (2011). Regulation of insulin-regulated membrane aminopeptidase activity by its C-terminal domain. Biochemistry, 50 (13), 2611-22. doi: 10.1021/bi101893w

Development of cognitive enhancers based on inhibition of insulin-regulated aminopeptidase

Chai, Siew Yeen, Yeatman, Holly R., Parker, Michael W., Ascher, David B., Thompson, Philip E., Mulvey, Hayley T. and Albiston, Anthony L. (2008). Development of cognitive enhancers based on inhibition of insulin-regulated aminopeptidase. BMC Neuroscience, 9 Suppl 2 (Supplement 2) S14. doi: 10.1186/1471-2202-9-S2-S14

Identification and characterization of a new cognitive enhancer based on inhibition of insulin-regulated aminopeptidase

Albiston, Anthony L, Morton, Craig J, Ng, Hooi Ling, Pham, Vi, Yeatman, Holly R, Ye, Siying, Fernando, Ruani N, De Bundel, Dimitri, Ascher, David B, Mendelsohn, Frederick A O, Parker, Michael W and Chai, Siew Yeen (2008). Identification and characterization of a new cognitive enhancer based on inhibition of insulin-regulated aminopeptidase. FASEB Journal, 22 (12), 4209-17. doi: 10.1096/fj.08-112227

Identification of modulating residues defining the catalytic cleft of insulin-regulated aminopeptidase

Ye, Siying, Chai, Siew Yeen, Lew, Rebecca A, Ascher, David B, Morton, Craig J, Parker, Michael W and Albiston, Anthony L (2008). Identification of modulating residues defining the catalytic cleft of insulin-regulated aminopeptidase. Biochemistry and Cell Biology, 86 (3), 251-61. doi: 10.1139/o08-037