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.
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A key limiting factor in organising and using information from [...]
BioExcel Whitepaper on Scientific Software Development (BioExcel-2 update)
This white paper presents the experience of the developers and recommendations for development of high-quality software engineering processes.
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We assess costs and efficiency of state-of-the-art high-performance cloud computing [...]
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Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine
Voltage-gated potassium channels of the Kv7.x family are involved in [...]