Phyre2.2

Phyre2.2 identifies suitable AlphaFold models to serve as templates for template-based protein structure prediction from amino acid sequences.

Key Features:

• AlphaFold Template Identification: Phyre2.2 identifies the most suitable AlphaFold model to be used as a template for modelling the query sequence.
• Expanded Template Library: The template library includes a representative structure for every protein sequence in the protein databank (PDB), with separate representatives for apo and holo structures when both are present in the PDB.
• Modified Hit Ranking: The ranking of hits highlights to the user if there are different domains spanning the sequence.
• Batch Processing: Phyre2.2 supports submission of up to 100 sequences for processing of proteomes.

Scientific Applications:

• Template-based Protein Structure Prediction: Phyre2.2 predicts protein structure from amino acid sequence by identifying sequence similarity to known structures for use as modelling templates.
• Proteome-scale Analysis: Batch processing of up to 100 sequences enables large-scale structural annotation of proteomes.
• Domain Architecture Analysis: Modified hit ranking highlights different domains spanning the query sequence to guide template selection.

Methodology:

Phyre2.2 searches a template library of known structures; the user submits a sequence and Phyre2.2 identifies the most suitable AlphaFold model to be used as a template.