Comparative structural analysis of protein complexes with SPICE

Computational tools for studying the structure of protein complexes are essential for providing mechanistic insights into protein-protein interactions and therapeutic drug design. Here, we present SPICE (Structural Protein Interaction Complex Evaluator), a web-based platform that allows structural biologists to perform rapid, modular analyses of protein complexes directly from Protein Data Bank (PDB) structures. SPICE allows users to define and execute analysis workflows via an intuitive web interface, reducing analysis times from minutes to seconds. The platform offers a broad range of analytical capabilities, including (i) detection of hydrogen bonds, salt bridges, and disulfide bonds; (ii) protein-protein interface mapping; and (iii) computation of solvent accessibility, van der Waals energetics, and other key geometric descriptors. SPICE further provides interactive 3D visualization and supports comparative analyses across multiple complexes, enabling the study of mutational effects and binding variants. The tool is freely available at https://spice.cs.ucr.edu (no registration required).