PROBind: A Web Server for Prediction, Analysis and Visualization of Protein-Protein and Protein-Nucleic Acid Binding Residues

Abstract

Protein-protein and protein-nucleic acids interactions are fundamental to numerous cellular functions, yet only a small fraction have been experimentally characterized. Although modern computational methods have been developed for predicting interacting residues in proteins, they are challenging to use due to individual installation and execution requirements, lack of a standardized input or output format, and absence of support for result analysis. Moreover, methods trained using structures of complexes or intrinsically disordered regions, may not perform well on other types. To overcome these challenges, we develop PROBind, a web server for predicting, analyzing, and interactively visualizing protein, DNA and RNA binding residues from both protein sequences and structures. PROBind integrates 12 predictors trained on structural or disordered proteins, and supports the upload of results from external predictors. By normalizing and averaging predictions from multiple predictors targeting the same ligand type, PROBind generates meta-predictions that balance discrepancies among different methods. Furthermore, it provides interactive graphical tools for result analysis and contextualization. Overall, PROBind accommodates diverse ligand types and supports predictions and analysis based on both structure and sequence data, overcoming the limitations of existing tools. PROBind is freely accessible at https://www.csuligroup.com/PROBind.