Fig. 1: Schematic of AlphaFold 3 mechanism.

AlphaFold 3 can predict the structure of proteins, DNA/RNA molecules, and ligands. 1) Once a sequence has been entered, 2) the software concurrently engages with multiple databases to assess potential genetic sequences, conformational prototypes, and structural configurations. 3) The input embedder then uses the sequencing and conformer information to encode and generate a composite that results in a single and pair representation. 4) The template module then integrates known structures obtained from the structural data search into the pair representation. 4/5) In tandem, the Multiple Sequence Alignment (MSA) Module incorporates the sequencing, pair representation, and template models to iteratively build novel base templates. 6) From here, the pairformer module uses MSA information to test different interacting elements, refining the predicted molecule interactions and repeatedly updating the pair and single representations. 7) Finally, the diffusion module applies and removes noise into the algorithm to improve local stereochemistry and global structures.