About Stian Soiland-Reyes

Stian works in School of Computer Science, at the University of Manchester in Carole Goble‘s eScience Lab as a technical software architect and researcher. In addition to BioExcel, Stian’s involvements include Open PHACTS (pharmacological data warehouse), Common Workflow Language (CWL), Apache Taverna (scientific workflow system), Linked Data and identifiers, research objects (open science) and digital preservation, myExperiment (sharing scientific workflows), provenance (where did things come from and who did it) and annotations (who said what). orcid.org/0000-0001-9842-9718

3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories

3D Representation Sharing (3dRS) is a web-based tool designed to share biomolecular structure representations, including 4D ensembles derived from Molecular Dynamics (MD) trajectories. The server offers a team working in different locations a single URL to share and discuss structural data in an interactive fashion, with the possibility to use it as a live figure for scientific papers. The web tool allows an easy upload of structures and trajectories in different formats.

By |2022-11-03T09:58:06+01:00August 13, 2021|Publications|Comments Off on 3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories
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Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue

Molecular docking excels at creating a plethora of potential models [...]

By |2022-11-03T09:58:06+01:00August 3, 2021|Publications|Comments Off on Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
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Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling

Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which [...]

By |2022-11-03T09:58:06+01:00July 20, 2021|Publications|Comments Off on Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling
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ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen and Data.

This project aims to develop a comprehensive W3C PROV based provenance information standard intended for the biomedical research domain.

By |2022-11-03T09:58:06+01:00July 9, 2021|Publications|Comments Off on ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen and Data.
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Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations

Here, we report cryo-electron microscopy (cryo-EM) structures of the proton-activated Gloeobacter violaceus ligand-gated ion channel (GLIC) under three pH conditions. Decreased pH was associated with improved resolution and side chain rearrangements at the subunit/domain interface, particularly involving functionally important residues in the β1–β2 and M2–M3 loops.

By |2022-11-03T09:58:06+01:00July 1, 2021|Publications|Comments Off on Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations
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Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN

Genome-wide localization of chromatin and transcription regulators can be detected [...]

By |2022-11-03T09:58:06+01:00May 21, 2021|Publications|Comments Off on Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN
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FUNDING


BioExcel is funded by the European Union Horizon 2020 program under grant agreements 823830, 675728 and by the EuroHPC Joint Undertaking and Sweden, Netherlands, Germany, Spain, Finland and Norway under grant agreement 101093290

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