• Protein Structure Prediction Paradigms:
• Statement (I): Ab initio method predicts protein structures based on sequence homology with known structures. $\implies$ False.
• Ab initio (de novo) structure prediction predicts 3D tertiary structure from physicochemical principles and amino acid sequences without using known homologous template structures.
• Statement (II): Homology modeling, also known as comparative modeling attempts to produce all-atom protein models based on sequence information alone without the aid of known protein structures. $\implies$ False.
• Homology (comparative) modeling constructs models strictly dependent on experimentally resolved 3D structures (templates from PDB) sharing significant sequence similarity.
• The definitions in the two statements are mutually inverted.
• Conclusion: Both Statement (I) and Statement (II) are false (Option 2).

Correct option: (2) Both Statement (I) and Statement (II) are false.

• RNA Secondary Structure Prediction Tools:
• mfold (developed by Michael Zuker) is the landmark thermodynamic energy-minimization algorithm used to predict RNA secondary structures (hairpins, stems, internal loops) by finding structures with minimum free energy (MFE, $\Delta G$).
• Other Tools Listed:
• RasMol: 3D macromolecular visualization software.
• GenTHREADER: Protein fold recognition (threading) software.
• RESTML: Maximum likelihood restriction site analysis tool.
• Conclusion: MFold (Option 2).

Correct option: (2) MFold