We have an open position for a Post-doctoral fellow interested in application of the cutting-edge molecular simulation methods to investigate mechanisms governing the transport of ligands in enzymes. The acquired knowledge will be crucial to enable discoveries of the molecular origins of transport-related pathologies, improvements of binding kinetics of lead-like compounds, and engineering of improved biocatalysts. The deadline for the application is March 24, 2021 but could be extended until a suitable candidate is found.
Sequeiros-Borja CE, Surpeta B, Brezovsky J, 2020: Recent advances in user-friendly computational tools to engineer protein function. Briefings in Bioinformatics. (Advance article DOI: 10.1093/bib/bbaa150) full text
Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein–protein and protein–nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.
Aravind has got one of eight awarded grants in the program of the Dean of Faculty of Biology. Many congratulations, and successful journey towards novel results!!!
Together with Artur Gora from Tunneling Group, we have been invited to guest-edit the special issue on Structure, Dynamics, and Function of Protein Tunnels and Channels in Life journal – CiteScore 2018 (Scopus) of 3.31. Looking forward to the experience.