Publications

Leak Proof CMap; a framework for training and evaluation of cell line agnostic L1000 similarity methods

Shave, S., Kasprowicz, R., Athar, A.M., Vlachou, D., Carragher, N.O., & Nguyen, C.Q. (2024). Leak Proof CMap; a framework for training and evaluation of cell line agnostic L1000 similarity methods.

Submitted: Repositioning Brusatol as a Transmission Blocker of the Malaria Parasite

Amelia Cox, Neelima Krishnakutty, Steven Shave, Virginia Howick, Manfred Auer, James La Clair, Nisha Philip. “Repositioning Brusatol as a Transmission Blocker of the Malaria Parasite”. SUBMITTED to ACS Infectious Disesases

Revealing the Indispensable Role of the RFamide Functionality using a Novel Acid Labile Benzofuranone based Amine (ALBA) Linker

Mudd, G., Hendrikse, M., Shave, S., Houston, D., Millar, R., & Auer, M. Revealing the Indispensable Role of the RFamide Functionality using a Novel Acid Labile Benzofuranone based Amine (ALBA) Linker. Helvetica Chimica Acta, e202300204.

From Intuition to AI: Evolution of Small Molecule Representations in Drug Discovery

Miles McGibbon, Steven Shave, Jie Dong, Yumiao Gao, Douglas Houston, Jiancong Xie, Yuedong Yang, Philippe Schwaller, and Vincent Blay. “From Intuition to AI: Evolution of Small Molecule Representations in Drug Discovery”. ACCEPTED in Briefings in Bioinformatics

OpenFEPOPS: A Python implementation of the FEPOPS molecular similarity technique

Chen, Y., Houston, D. R., Auer, M., & Shave, S. (2023). OpenFEPOPS: A Python implementation of the FEPOPS molecular similarity technique. Journal of Open Source Software, 8(91), 5763.

Evolution and impact of high content imaging

Gregory Way, Heba Sailem, Steven Shave, Richard Kasprowicz, Neil Carragher, “Evolution and impact of high content imaging.” Slas Discovery, 2023.

Phenonaut: multiomics data integration for phenotypic space exploration

Steven Shave, John Dawson, Abdullah Athar, Cuong Nguyen, Richard Kasprowicz, Neil Carragher, “Phenonaut: multiomics data integration for phenotypic space exploration.” Bioinformatics, 2023.

Chemical interrogation of nuclear size identifies compounds with cancer cell line-specific effects on migration and invasion

Sylvain Tollis, Andrea Rizzotto, Nhan Pham, Sonja Koivukoski, Aishwarya Sivakumar, Steven Shave, Jan Wildenhain, Nikolaj Zuleger, Jeremy Keys, Jayne Culley, Yijing Zheng, Jan Lammerding, Neil Carragher, Valerie Brunton, Leena Latonen, Manfred Auer, Mike Tyers, Eric Schirmer, “Chemical interrogation of nuclear size identifies compounds with cancer cell line-specific effects on migration and invasion.” ACS chemical biology, 2022.

CLAffinity: A Software Tool for Identification of Optimum Ligand Affinity for Competition-Based Primary Screens

Steven Shave, Nhan Pham, Manfred Auer, “CLAffinity: A Software Tool for Identification of Optimum Ligand Affinity for Competition-Based Primary Screens.” Journal of Chemical Information and Modeling, 2022.

SimilarityLab: molecular similarity for SAR exploration and target prediction on the web

Steven Shave, Manfred Auer, “SimilarityLab: molecular similarity for SAR exploration and target prediction on the web.” Processes, 2021.

Mrlogp: transfer learning enables accurate logp prediction using small experimental training datasets

Yan-Kai Chen, Steven Shave, Manfred Auer, “Mrlogp: transfer learning enables accurate logp prediction using small experimental training datasets.” Processes, 2021.

PyBindingCurve, simulation, and curve fitting to complex binding systems at equilibrium

Steven Shave, Yan-Kai Chen, Nhan Pham, Manfred Auer, “PyBindingCurve, simulation, and curve fitting to complex binding systems at equilibrium.” Journal of Chemical Information and Modeling, 2021.

A two-step resin based approach to reveal survivin-selective fluorescent probes

Ambrose, Andrew J., et al. “A two-step resin based approach to reveal survivin-selective fluorescent probes.” RSC Chemical Biology 2.1 (2021): 181-186.

Quantitative microdialysis: experimental protocol and software for small molecule protein affinity determination and for exclusion of compounds with poor physicochemical properties

Shave, Steven, et al. “Quantitative microdialysis: experimental protocol and software for small molecule protein affinity determination and for exclusion of compounds with poor physicochemical properties.” Methods and Protocols 3.3 (2020): 55.

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D

Kennedy, Susan A., et al. “Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D.” Nature communications 11.1 (2020): 499.

Diclofenac identified as a kynurenine 3-monooxygenase binder and inhibitor by molecular similarity techniques

Shave, Steven, et al. “Diclofenac identified as a kynurenine 3-monooxygenase binder and inhibitor by molecular similarity techniques.” ACS omega 3.3 (2018): 2564-2568.

PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries

Shave, Steven, et al. “PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries.” PLoS One 13.2 (2018): e0193332.

Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay

Koszela, J., Pham, N. T., Evans, D., Mann, S., Perez-Pi, I., Shave, S., … & Auer, M. (2018). Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay. BMC biology, 16(1), 1-13.

Inhibition of the ERCC1XPF structure-specific endonuclease to overcome cancer chemoresistance

McNeil, Ewan M., Katy R. Astell, Ann-Marie Ritchie, Steven Shave, Douglas R. Houston, Preeti Bakrania, Hayley M. Jones et al. “Inhibition of the ERCC1XPF structure-specific endonuclease to overcome cancer chemoresistance.” DNA repair 31 (2015): 19-28.

UFSRAT: ultra-fast shape recognition with atom typesthe discovery of novel bioactive small molecular scaffolds for FKBP12 and 11?HSD1

Shave, S., Blackburn, E. A., Adie, J., Houston, D. R., Auer, M., Webster, S. P., … & Walkinshaw, M. D. (2015). UFSRAT: ultra-fast shape recognition with atom typesthe discovery of novel bioactive small molecular scaffolds for FKBP12 and 11?HSD1. PLoS One, 10(2), e0116570.

Identification and X?ray co?crystal structure of a small?molecule activator of LFA?1?ICAM?1 binding

Hintersteiner, Martin, Joerg Kallen, Mario Schmied, Christine Graf, Thomas Jung, Gemma Mudd, Steven Shave, Hubert Gstach, and Manfred Auer. “Identification and X?ray co?crystal structure of a small?molecule activator of LFA?1?ICAM?1 binding.” Angewandte Chemie International Edition 53, no. 17 (2014): 4322-4326.

High-throughput chemical screening for antivirulence developmental phenotypes in Trypanosoma brucei

MacGregor, P., Ivens, A., Shave, S., Collie, I., Gray, D., Auer, M., & Matthews, K. R. (2014). High-throughput chemical screening for antivirulence developmental phenotypes in Trypanosoma brucei. Eukaryotic Cell, 13(3), 412-426.

CSBB-ConeExclusion, adapting structure based solution virtual screening to libraries on solid support

Shave, Steven, and Manfred Auer. “CSBB-ConeExclusion, adapting structure based solution virtual screening to libraries on solid support.” Journal of chemical information and modeling 53.12 (2013): 3156-3162.

11?-Hydroxysteroid dehydrogenase type 1 contributes to the balance between 7-keto-and 7-hydroxy-oxysterols in vivo

Mitic, Tijana, Steven Shave, Nina Semjonous, Iain McNae, Diego F. Cobice, Gareth G. Lavery, Scott P. Webster, Patrick WF Hadoke, Brian R. Walker, and Ruth Andrew. “11?-Hydroxysteroid dehydrogenase type 1 contributes to the balance between 7-keto-and 7-hydroxy-oxysterols in vivo.” Biochemical Pharmacology 86, no. 1 (2013): 146-153.

Discovery of a new class of inhibitors for the protein arginine deiminase type 4 (PAD4) by structure-based virtual screening

Teo, C. Y., Shave, S., Thean Chor, A. L., Salleh, A. B., Abdul Rahman, M. B. B., Walkinshaw, M. D., & Tejo, B. A. (2012, December). Discovery of a new class of inhibitors for the protein arginine deiminase type 4 (PAD4) by structure-based virtual screening. In BMC bioinformatics (Vol. 13, No. 17, pp. 1-13). BioMed Central.

Steven Shave