Shape-Restrained Modeling of Protein–Small-Molecule Complexes with High Ambiguity Driven DOCKing
Small-molecule docking remains one of the most valuable computational techniques [...]
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.
Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
Molecular docking excels at creating a plethora of potential models [...]
Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling
Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which [...]
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.
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.
