About
I’m a computational biologist focused on understanding how human genetic variation…
Contributions
Activity
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March update to the Protein Design Archive (https://lnkd.in/efsQe7WY) 🚀 14 new designed protein structures have been added ➡️ Highlights include:…
March update to the Protein Design Archive (https://lnkd.in/efsQe7WY) 🚀 14 new designed protein structures have been added ➡️ Highlights include:…
Liked by Stuart MacGowan
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Really cool. Definitely would come in handy when dealing with 100s of structures!
Really cool. Definitely would come in handy when dealing with 100s of structures!
Liked by Stuart MacGowan
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Exciting opportunity (below) for a Computational Biologist (Research Associate and Research Assistant) to work on a project involving the analysis of…
Exciting opportunity (below) for a Computational Biologist (Research Associate and Research Assistant) to work on a project involving the analysis of…
Liked by Stuart MacGowan
Experience
Education
Licenses & Certifications
Volunteer Experience
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Simulated Patient
University of Dundee
- 1 year 1 month
Education
I helped train future doctors and other health professionals by playing the part of the patient in clinical training scenarios.
Publications
Projects
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Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP)
The Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP) is a collaborative effort to provide a comprehensive suite of tools for the analysis of protein sequences and structures. Developed by the Barton Group at the University of Dundee, DRSASP offers various web services, APIs, and integration with the Jalview sequence analysis workbench.
DRSASP's flagship services include the JPred4 webserver for secondary structure and solvent accessibility prediction, and the…The Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP) is a collaborative effort to provide a comprehensive suite of tools for the analysis of protein sequences and structures. Developed by the Barton Group at the University of Dundee, DRSASP offers various web services, APIs, and integration with the Jalview sequence analysis workbench.
DRSASP's flagship services include the JPred4 webserver for secondary structure and solvent accessibility prediction, and the JABAWS 2.2 webserver for multiple sequence alignment, disorder prediction, amino acid conservation calculations, and specificity-determining site prediction. Other tools within DRSASP are AACon, NoD, 14-3-3-Pred, Xtal, Kinomer, and AMAS.
Our goal is to address a wide range of questions relevant to novel protein sequences, such as protein structure, disorder, crystallization, amino acid conservation, functional specificity, cellular localization, and protein-protein interactions. DRSASP is an Elixir-UK Tier 1 Resource, signifying its importance in the strategic area of Protein Structure and Function.
Ongoing developments aim to improve DRSASP's efficiency in whole proteome analyses, enhance interoperability and reproducibility, and optimize testing and portability. We are actively working on integrating modern technologies like containerization (e.g., Docker) and dependency management solutions (e.g., Conda) to simplify maintenance workflows and ensure reproducibility. Continuous monitoring and end-to-end interface tests for our services also contribute to the overall reliability of DRSASP.
Through this project, we strive to provide valuable computational resources to the scientific community and facilitate the analysis of protein sequences and structures for researchers worldwide.Other creatorsSee project -
Integrating population and evolutionary variation in proteins
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Experimental Validation of the Effects of Human ACE2 Variants on SARS-CoV-2 Spike Binding
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Building on earlier computational predictions, this project involved experimental validation of the impact of human ACE2 variants on binding to the SARS-CoV-2 Spike protein. By selecting 10 ACE2 variants based on affinity predictions and prevalence in gnomAD, the study used surface plasmon resonance (SPR) to measure their affinities and kinetics for the Spike receptor binding domain. The research identified variants that both reduce and enhance binding, providing insights into potential genetic…
Building on earlier computational predictions, this project involved experimental validation of the impact of human ACE2 variants on binding to the SARS-CoV-2 Spike protein. By selecting 10 ACE2 variants based on affinity predictions and prevalence in gnomAD, the study used surface plasmon resonance (SPR) to measure their affinities and kinetics for the Spike receptor binding domain. The research identified variants that both reduce and enhance binding, providing insights into potential genetic risk factors for COVID-19 susceptibility and severity. The study also assessed the utility of the mCSM-PPI2 ΔΔG predictions in comparison to the experimental SPR data.
Other creatorsSee project -
Rapid Analysis of ACE2 Variants and Their Impact on SARS-CoV-2 Spike Binding
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This project involved an intensive month of research to investigate the effects of ACE2 missense variants on the binding of SARS-CoV-2 Spike protein. By validating the mCSM-PPI2 variant effect prediction algorithm and applying it to ACE2 missense variants from the Genome Aggregation Consortium Database (gnomAD), the study identified several key variants that could either inhibit or enhance the interaction between ACE2 and the SARS-CoV-2 Spike protein. This work provided valuable insights into…
This project involved an intensive month of research to investigate the effects of ACE2 missense variants on the binding of SARS-CoV-2 Spike protein. By validating the mCSM-PPI2 variant effect prediction algorithm and applying it to ACE2 missense variants from the Genome Aggregation Consortium Database (gnomAD), the study identified several key variants that could either inhibit or enhance the interaction between ACE2 and the SARS-CoV-2 Spike protein. This work provided valuable insights into potential genetic risk factors for COVID-19 susceptibility and severity and suggested strategies for designing recombinant ACE2 with tailored affinity towards the Spike protein.
Honors & Awards
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p2i in Action Paris Entrepreneurial Training Week Participant (Award Recipient)
p2i Network
Selected as one of the participants for the prestigious p2i in Action Paris Entrepreneurial Training Week in 2022. Engaged in intensive learning, networking, and skill-building sessions with a diverse group of entrepreneurs and innovators from around the world. This week-long program developed my entrepreneurial knowledge and provided invaluable insights into business strategies, innovation, and leadership.
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Best poster at School of Life Sciences Crieff Retreat 2018
School of Life Sciences, University of Dundee
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Trinity College Dublin's nominee for the 63rd Lindau Nobel Laureate Meeting
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Best presentation at Dublin Chemistry Student Symposium
School of Chemistry, Trinity College Dublin
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Ivan L. S. Allen Medal
University of the West of Scotland
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University Court Medal for most distinguished student in Chemistry
University of the West of Scotland
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University Court Medal for most distinguished student in Chemistry
University of the West of Scotland
More activity by Stuart
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🌟Uni-Dock License Update to Apache 2.0🌟 We are pleased to announce that Uni-Dock is now officially licensed under Apache 2.0! 🎉A big THANK YOU to…
🌟Uni-Dock License Update to Apache 2.0🌟 We are pleased to announce that Uni-Dock is now officially licensed under Apache 2.0! 🎉A big THANK YOU to…
Liked by Stuart MacGowan
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In a new Practical Cheminformatics post titled "Even More Thoughts on ML Method Comparisons," I share several plots that I find valuable for…
In a new Practical Cheminformatics post titled "Even More Thoughts on ML Method Comparisons," I share several plots that I find valuable for…
Liked by Stuart MacGowan
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