BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools
BioBB REST API extends and complements the BioBB library offering programmatic access to the collection of biomolecular simulation tools included in the BioExcel Building Blocks library. Molecular Dynamics setup, docking, structure modeling, free energy simulations, and flexibility analyses are examples of functionalities included in the endpoints collection. All functionalities are accessible through standard REST API calls, voiding the need for tool installation.
Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel
Pentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in [...]
Prediction Of The Impact Of Genetic Variability On Drug Sensitivity For Clinically Relevant EGFR Mutations
Mutations in the kinase domain of the Epidermal Growth Factor [...]
Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators
The α7 nicotinic acetylcholine receptor is a pentameric ligand-gated ion [...]
Interface refinement of low- to medium-resolution Cryo-EM complexes using HADDOCK2.4
A wide range of cellular processes requires the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The density maps produced can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low- to medium-resolution maps. Unfortunately, the models produced frequently contain atomic clashes at the protein-protein interfaces (PPIs), as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols.
The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections GalleryThe Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections
The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections
A key limiting factor in organising and using information from [...]
