MarkUs

MarkUs analyzes and compares structural and functional properties of proteins to suggest and evaluate protein functions and support hypothesis generation.

Key Features:

• Structural and functional comparison: Compares structural features and functional annotations of protein structures to identify correspondences and discrepancies.
• Similarity-based function suggestion: Employs various similarity measures to automatically suggest possible protein functions based on structural and annotation similarities.
• User-provided function hypotheses: Accepts and incorporates user-specified function hypotheses for comparative evaluation against computed predictions.
• Independent assessment against bioinformatic and biophysical properties: Provides analyses that evaluate whether suggested functions align with bioinformatic evidence and biophysical properties of the query structure.
• Hypothesis generation: Integrates structural insights and functional predictions to generate testable biological hypotheses about protein function.

Scientific Applications:

• Protein function annotation: Supports annotation of proteins by proposing and evaluating candidate functions beyond sequence-based inference.
• Structural biology research: Facilitates investigation of relationships between protein structure and biological activity through comparative analyses.
• Drug discovery and development: Aids identification and evaluation of potential protein targets by relating structural features to functional implications.

Methodology:

Uses bioinformatic algorithms and biophysical principles and employs various similarity measures to analyze protein structures, suggest functions, accept user-specified function hypotheses, and assess consistency with bioinformatic and biophysical properties.