IntelliFold-2: Surpassing AlphaFold 3 via Architectural Refinement and Structural Consistency

Abstract

IntelliFold-2 is an open-source biomolecular structure prediction model that improves accuracy and robustness through architectural refinement and multiscale structural consistency. We introduce latent space scaling in Pairformer blocks, a principled atom-attention formulation with stochastic atomization, policy-guided optimization for diffusion sampling and difficulty-aware loss reweighting. On Foldbench, IntelliFold-2 improves performance in therapeutically relevant settings, with particularly strong gains for antibody-antigen interactions and protein-ligand co-folding relative to AlphaFold 3. We release three variants (Flash, v2, and Pro) to cover efficient fine-tuning through high-precision server-side inference.