AIDA

AIDA assembles and predicts multi-domain protein structures using ab initio domain assembly to determine domain boundaries and relative domain arrangements.

Key Features:

• Domain identification and prediction: Identifies domains from sequence or from user-provided domain assignments and determined domain boundaries for 97% of targets in CASP10.
• Ab initio folding potential: Uses an ab initio folding potential to guide assembly and to model domain–domain interactions when no full-length homologous templates are available.
• Support for discontinuous domains: Assembles continuous and discontinuous domains, including inserted domains, to represent complex domain architectures.
• Restraint-guided simulation: Incorporates user-specified inter-domain distance restraints to guide energy minimization during assembly.
• Benchmark performance: Identified accurate relative domain positions among the top 5000 models in 86% of tested experimentally solved multi-domain proteins.

Scientific Applications:

• Multi-domain structure prediction: Predicts three-dimensional configurations of multi-domain proteins from sequence-derived domain models.
• Functional and interaction inference: Provides domain arrangements to inform analyses of protein function and protein–protein interaction networks.
• Evolutionary and architectural studies: Supports investigation of domain reshuffling and evolutionary relationships by resolving domain boundaries and architectures.
• Stability and mechanism hypotheses: Generates spatial-domain hypotheses relevant to protein stability and functional mechanisms.

Methodology:

Domain detection from sequence; ab initio prediction of individual domain 3D structures; assembly of predicted domain structures into complete protein models guided by an ab initio folding potential and optionally by inter-domain distance restraints.