AlphaFill

AlphaFill augments AlphaFold-predicted protein structures by transplanting missing small molecules, metal ions, ligands, and cofactors from experimentally determined structures using sequence and structure similarity to restore biologically relevant molecular contexts.

Key Features:

• Transplantation of Missing Molecules: Transplants metal ions, ligands, and cofactors from experimentally determined structures into predicted models based on sequence and structure similarity.
• Enhanced Functional Insight: Incorporates molecular contexts such as heme in hemoglobin and zinc ions in zinc-finger motifs to inform structural integrity and function.
• Extensive Validation: Validates transplanted molecules by comparison with experimental structures and associated validation metrics.
• Large-Scale Application: Performed 12,029,789 transplants across 995,411 AlphaFold models.
• Databank with Validation Metrics: Stores transplant results and validation metrics in the alphafill.eu databank.

Scientific Applications:

• Structural Biology: Enables analysis of protein folding, stability, and interactions by restoring bound small molecules and ions in structural models.
• Drug Discovery: Reveals potential small-molecule binding sites in enhanced models to support target identification and ligand design.
• Enzyme Engineering: Provides precise positions of metal ions and cofactors to inform engineering of catalytic properties and substrate specificity.
• Functional Genomics: Connects genetic variation to structural effects by supplying detailed molecular contexts for interpretation of mutational impacts.

Methodology:

Uses sequence and structure similarity to identify missing small molecules or ions in AlphaFold predictions; selects donor molecules from a curated set of experimentally determined structures; algorithmically transplants and orients donors into predicted models preserving interactions with surrounding amino acids; validates enhanced models against experimental data and reports validation metrics.