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

Authors: Shave, Steven, Kasprowicz, Richard, Athar, Abdullah M., Vlachou, Denise, Carragher, Neil O., Nguyen, Cuong Q.

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2404.18960

Evolution and impact of high content imaging

Authors: Way, Gregory P., Sailem, Heba, Shave, Steven, Kasprowicz, Richard, Carragher, Neil O.

Source: In SLAS Discovery October 2023 28(7):292-305

From intuition to AI: evolution of small molecule representations in drug discovery.

Authors: McGibbon, Miles¹ (AUTHOR), Shave, Steven¹ (AUTHOR), Dong, Jie² (AUTHOR), Gao, Yumiao¹ (AUTHOR), Houston, Douglas R¹ (AUTHOR), Xie, Jiancong³ (AUTHOR), Yang, Yuedong³ (AUTHOR), Schwaller, Philippe⁴ (AUTHOR), Blay, Vincent¹ (AUTHOR) v1vblay@ed.ac.uk

Source: Briefings in Bioinformatics. Jan2024, Vol. 25 Issue 1, p1-13. 13p.

Subject Terms: *DRUG discovery, *SMALL molecules, *ARTIFICIAL intelligence, *HUMAN fingerprints, *INTUITION, *MACHINE learning

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

Authors: Shave, Steven, Pham, Nhan T., Auer, Manfred

Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 62(10):2264-2268

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632696842&indx=1&recIds=ETOCRN632696842

Chemical Interrogation of Nuclear Size Identifies Compounds with Cancer Cell Line-Specific Effects on Migration and Invasion

Authors: Tollis, Sylvain, Rizzotto, Andrea, Pham, Nhan T., Koivukoski, Sonja, Sivakumar, Aishwarya, Shave, Steven, Wildenhain, Jan, Zuleger, Nikolaj, Keys, Jeremy T., Culley, Jayne

Source: ACS chemical biology. 17(3):680-700

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN628905573&indx=1&recIds=ETOCRN628905573

Cellular Activity of CQWW Nullomer-Derived Peptides.

Authors: Shave, Steven, Isaksson, Rebecka, Pham, Nhan T., Elliott, Richard J. R., Dawson, John C., Soudant, Julius, Carragher, Neil O., Auer, Manfred

Source: ACS Omega; 2/25/2025, Vol. 10 Issue 7, p6794-6800, 7p

PyBindingCurve, Simulation, and Curve Fitting to Complex Binding Systems at Equilibrium

Authors: Shave, Steven, Chen, Yan-Kai, Pham, Nhan T., Auer, Manfred

Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 61(6):2911-2915

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632695201&indx=1&recIds=ETOCRN632695201

A two-step resin based approach to reveal survivin-selective fluorescent probesElectronic supplementary information (ESI) available: Experimental procedures, additional data and supplementary figures. See DOI: 10.1039/d0cb00122h

Authors: Ambrose, Andrew J., Pham, Nhan T., Sivinski, Jared, Guimarães, Larissa, Mollasalehi, Niloufar, Jimenez, Paula, Abad, Maria A., Jeyaprakash, A. Arockia, Shave, Steven, Costa-Lotufo, Letícia V., La Clair, James J., Auer, Manfred, Chapman, Eli

Source: RSC chemical biology. 2(1):181-186

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100128495801.0x000001&indx=1&recIds=ETOCvdc_100128495801.0x000001

A Novel Confocal Scanning Protein–Protein Interaction Assay (PPI-CONA) Reveals Exceptional Selectivity and Specificity of CC0651, a Small Molecule Binding Enhancer of the Weak Interaction between the E2 Ubiquitin-Conjugating Enzyme CDC34A and Ubiquitin

Authors: Koszela, Joanna, Pham, Nhan T., Shave, Steven, St-Cyr, Daniel, Ceccarelli, Derek F., Orlicky, Steven, Marinier, Anne, Sicheri, Frank, Tyers, Mike, Auer, Manfred

Source: Bioconjugate Chemistry; September 2024, Vol. 35 Issue: 9 p1441-1449, 9p

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

Authors: Mudd, Gemma¹, Hendrikse, Megan², Shave, Steven¹, steven.shave@ed.ac.uk, Houston, Douglas R¹, Millar, Robert P^2,3, Auer, Manfred¹, manfred.auer@ed.ac.uk

Source: Helvetica Chimica Acta; Apr2024, Vol. 107 Issue 4, p1-7, 7p

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

Authors: Koszela, Joanna, Pham, Nhan, Evans, David, Mann, Stefan, Perez-Pi, Irene, Shave, Steven, Ceccarelli, Derek, Sicheri, Frank, Tyers, Mike, Auer, Manfred

Source: BMC biology. 16(1):1-13

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100174890025.0x000001&indx=1&recIds=ETOCvdc_100174890025.0x000001

Inhibition of the ERCC1–XPF structure-specific endonuclease to overcome cancer chemoresistance

Authors: McNeil, Ewan M., Astell, Katy R., Ritchie, Ann-Marie, Shave, Steven, Houston, Douglas R., Bakrania, Preeti, Jones, Hayley M., Khurana, Puneet, Wallace, Claire, Chapman, Tim, Wear, Martin A., Walkinshaw, Malcolm D., Saxty, Barbara, Melton, David W.

Source: In DNA Repair July 2015 31:19-28

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

Authors: Mitić, Tijana, Shave, Steven, Semjonous, Nina, McNae, Iain, Cobice, Diego F., Lavery, Gareth G., Webster, Scott P., Hadoke, Patrick W.F., Walker, Brian R., Andrew, Ruth

Source: In Biochemical Pharmacology 1 July 2013 86(1):146-153

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

Authors: Kennedy, Susan A., Jarboui, Mohamed-Ali, Srihari, Sriganesh, Raso, Cinzia, Bryan, Kenneth, Dernayka, Layal, Charitou, Theodosia, Bernal-Llinares, Manuel, Herrera-Montavez, Carlos, Krstic, Aleksandar, Matallanas, David, Kotlyar, Max, Jurisica, Igor, Curak, Jasna, Wong, Victoria, Stagljar, Igor, LeBihan, Thierry, Imrie, Lisa, Pillai, Priyanka, Lynn, Miriam A., Fasterius, Erik, Al-Khalili Szigyarto, Cristina, Breen, James, Kiel, Christina, Serrano, Luis, Rauch, Nora, Rukhlenko, Oleksii, Kholodenko, Boris N., Iglesias-Martinez, Luis F., Ryan, Colm J., Pilkington, Ruth, Cammareri, Patrizia, Sansom, Owen, Shave, Steven, Auer, Manfred, Horn, Nicola, Klose, Franziska, Ueffing, Marius, Boldt, Karsten, Lynn, David J., Kolch, Walter

Source: Nature communications. 11(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131053572.0x000001&indx=1&recIds=ETOCvdc_100131053572.0x000001

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

Authors: Teo Chian, Shave Steven, Thean Chor Adam, Salleh Abu, Abdul Rahman Mohd Basyaruddin, Walkinshaw Malcolm D, Tejo Bimo A

Source: BMC Bioinformatics, Vol 13, Iss Suppl 17, p S4 (2012)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/914b517a39a04b5e9b2bfe1e2693eb3e

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

Authors: Shave, Steven¹ s.shave@ed.ac.uk, Mann, Stefan¹, Koszela, Joanna¹, Kerr, Alastair¹, Auer, Manfred¹ manfred.auer@ed.ac.uk

Source: PLoS ONE. 2/23/2018, Vol. 13 Issue 2, p1-10. 10p.

Subject Terms: *NUCLEOTIDE sequencing, *BIOINFORMATICS, *AMINO acid sequence, *PROTEOMICS, *COMPUTATIONAL biology

UFSRAT: Ultra-Fast Shape Recognition with Atom Types –The Discovery of Novel Bioactive Small Molecular Scaffolds for FKBP12 and 11βHSD1.

Authors: Shave, Steven¹, Blackburn, Elizabeth A.¹, Adie, Jillian¹, Houston, Douglas R.¹, Auer, Manfred¹, Webster, Scott P.², Taylor, Paul¹, Walkinshaw, Malcolm D.¹ m.walkinshaw@ed.ac.uk

Source: PLoS ONE. Feb2015, Vol. 10 Issue 2, p1-15. 15p.

Subject Terms: *HYDROXYSTEROID dehydrogenases, *MOLECULAR recognition, *BIOACTIVE compounds, *CARRIER proteins, *SMALL molecules, *SCAFFOLDING

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Phenonaut: multiomics data integration for phenotypic space exploration.

Authors: Shave, Steven^1,2 (AUTHOR) s.shave@ed.ac.uk, Dawson, John C² (AUTHOR), Athar, Abdullah M¹ (AUTHOR), Nguyen, Cuong Q³ (AUTHOR), Kasprowicz, Richard¹ (AUTHOR), Carragher, Neil O² (AUTHOR) n.carragher@ed.ac.uk

Source: Bioinformatics. Apr2023, Vol. 39 Issue 4, p1-2. 2p.

Subject Terms: *DATA integration, *MULTIOMICS, *SOURCE code, *INTEGRATED software, *PHENOTYPES, *PYTHON programming language, *SPACE exploration

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