Software Involved in Simulation

　AlphaFold3 is an advanced AI model, building upon the foundational progress of AlphaFold2, designed for high-precision prediction of biomolecular structures and interactions. This model extends its applicability beyond protein structures to include a broad spectrum of molecular interactions, encompassing DNA, RNA, and small-molecule ligands.

Several data–such as 3D structure of the protein, assesments of structural rigidity and flexibility, and detailed infromation on molecular interactions–is obtainable by inputting an amino acid sequence into AlphaFold3. It is deemed a powerful tool for understanding complex biological system utilizing this expanded functionality.

Inputting an amino acid sequence and pressing "Continue and preview job" will execute the computational process of which the results are shown below.

PyMOL is an open-source molecular visualization tool designed for analyzing the 3D structures of proteins and other biomolecules. It enables the 3D visualization of a wide range of molecules, including proteins, DNA, RNA, and small molecules. Users can highlight specific structural features, such as α-helices and β-sheets, and easily toggle the display of regions of interest, such as binding sites. The software also allows for interactive manipulation of molecular structures, including rotation, zooming, and translation, as well as the measurement of distances and angles between residues. PyMOL is an essential tool for detailed protein visualization and structural analysis.