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- Stage I: INPUT FILE PREPARATIONS FOR BHAGEERATH+
- Stage II: SEQUENCE BASED FEATURES CALCULATION
- Stage III: SECONDARY STRUCTURE PREDICTION
- Stage IV: HOMOLOGY DETECTION AND ALIGNMENT GENERATION
- Stage V: DECOY STRUCTURE GENERATION
- Stage VI: FRAGMENT ASSEMBLY AND AB INITIO LOOP SAMPLING
- Stage VII: QUALITY ASSESSMENT OF GENERATED MODEL STRUCTURES
- Stage VIII: ENERGY MINIMIZATION AND SIDE CHAIN OPTIMIZATION OF TOP5 MODEL STRUCTURES