Residue interaction networks

Proteins, as large macromolecules, exhibit intricate three-dimensional structures and dynamic motions that enable them to perform various cellular functions. These functions rely on non-covalent interactions, which contribute to the stability of folded structures, facilitate interactions with other molecules, and play vital roles in molecular communication, such as allosterism and signaling processes, often mediated by transient interactions.

To better understand protein structures and interactions, our lab employs network theory as an alternative approach. We utilize Residue Interaction Networks (RINs), also known as Protein Structure Networks (PSNs), which represent amino acids as nodes and the connections between them as edges. By defining these connections based on physico-chemical properties and geometric constraints, we can analyze the network properties and characterize specific types of interactions.

Our lab offers a range of solutions for the analysis of RINs, with particular emphasis on the Residue Interaction Network Generator (RING).
Since 2011, we have been developing and maintaining RING, which has proven highly successful in numerous studies across various areas of protein research. RING has contributed to investigations on binding and allosterism, interfaces, protein stability, protein engineering, ligand binding prediction, software development, and molecular dynamics analysis.

RING has been employed to explore the relationship between the size of protein complex interfaces and the likelihood of cotranslational assembly. By utilizing RING, contact-related properties of the interfaces were calculated, allowing for a characterization of different interaction types between subunits.

Furthermore, RING is extensively used for structural ensemble analysis. It enables the analysis of molecular dynamics simulations by calculating probabilistic contact networks and facilitates investigations into protein stability and virtual screening. The versatility of RING has made it a valuable tool in the field.

RING detects various types of interactions, including hydrogen bonding, π-π stacking, π-cation, van der Waals, π-hydrogen and halogen bonds, as well as metal ion coordination. The comprehensive interaction networks provided by RING encompass a wide range of combinations, including proteins, nucleotides, lipids, ligands, and small molecules. RING is available as a web server, C++ executable and PyMol plugin. The new server includes improved visualization tools, additional data, and a faster calculation speed. The underlying software library has been optimized to process all the chemical compounds available in the PDB chemical component dictionary, encompassing over 35,000 different molecules. These interactions can be visualized simultaneously in the structure viewer and in a graph representation, offering a comprehensive understanding of the protein’s structural landscape.

We invite you to explore RING and leverage its powerful capabilities to gain deeper insights into protein structures, interactions, and their functional implications. Our user-friendly interface and advanced features will empower you to unravel the complexities of the protein world with unprecedented clarity.