New tool for visualizing molecule properties developed at the Max Perutz Labs

Nucleic acids and proteins can be described on different structural levels, but all depend on the most basic - the primary structure. It describes the exact sequence of amino acids or nucleotides – the smallest molecular units that form proteins or RNA and DNA. These units have certain physical and chemical properties, like charge or propensity to interact with water, which ultimately determine the property and, therefore, the function of the whole molecule.

Lukas Bartonek and Bojan Zagrovic at Max Perutz Labs have now developed VOLPES (Visualization of Physicochemical Sequence Properties), a free-to-use, web-based tool to visualize and explore the sequence properties of proteins and nucleic acids in an interactive manner. The server utilizes publicly available sequences and combines them with detailed descriptors of over 600 different physiochemical properties. Real-time manipulation of the data allows researchers to identify correlations in these properties that may not be apparent if only the primary structure is considered.

This enables the user to find out if and why different proteins, RNA or DNA molecules behave in a similar manner despite having very dissimilar sequences. Since many important molecular properties, like localization in the cell, propensity to interact with different partners or adopt a particular molecular shape, depend on the properties covered by the tool, the authors hope it will find a wide range of applications in different areas of biological research: “Biological sequences ultimately refer to real, physical objects and the aim of VOLPES is to enable researchers to easily visualize and compare the properties of these objects”, group leader Bojan Zagrovic concludes.