aTOME-2

aTOME-2 performs protein structure modeling and small-ligand docking using comparative analyses to predict three-dimensional protein structures and explore protein–ligand interactions.

Key Features:

• Sequence input: Accepts protein sequences in one-letter amino-acid code.
• Fold recognition: Performs fold recognition from amino-acid sequence data.
• Template selection: Selects structural templates for comparative modeling.
• Structural alignment editing: Provides editing of structural alignments for model building.
• Structure comparisons: Conducts comparisons between protein structures and templates.
• 3D-model building: Builds three-dimensional protein models based on selected templates and alignments.
• Model evaluation: Evaluates generated protein models.
• Comparative ligand docking: Performs comparative docking of small ligands using protein–protein superposition techniques.
• Outputs: Produces 3D protein models, protein–ligand complex models, and structural alignments.

Scientific Applications:

• Functional annotation: Supports structural inference for protein functional annotation.
• Template selection for modeling: Aids selection of appropriate templates for molecular modeling studies.
• Virtual screening: Enables comparative approaches for virtual screening of small ligands.
• Protein–ligand interaction exploration: Facilitates analysis of potential protein–ligand interactions to inform molecular function and drug discovery.

Methodology:

Accepts a one-letter amino-acid sequence and applies fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building, model evaluation, and comparative small-ligand docking via protein–protein superposition.