Author
Stian Soiland-Reyes

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. [...]

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. [...]

Enabling the execution of large scale workflows for molecular dynamics simulations

In this paper we present an approach to support biomolecular researchers in the development of complex workflows. Our approach is based on the orchestration of computational building blocks for Molecular Dynamics simulations through an efficient workflow management system that has already been adopted in many scientific fields to run applications on multitudes of computing backends. [...]

Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

To serve the needs of this established and diverse community, EOSC-Life has developed WorkflowHub as an inclusive workflow registry, agnostic to any Workflow Management System (WfMS). WorkflowHub aims to incorporate their workflows in partnership with the WfMS, to embed the registration of workflows in the community processes, e.g. based on pre-existing workflow repositories. [...]