Depending on whether similar structures are found in the PDB library, the protein structure prediction can be categorized into template-based modeling and free modeling. Although threading is an efficient tool to detect the structural analogs, the advancements in methodology development have come to a steady state. Encouraging progress is observed in structure refinement which aims at drawing template structures closer to the native; this has been mainly driven by the use of multiple structure templates and the development of hybrid knowledge-based and physics-based force fields. For free modeling, exciting examples have been witnessed in folding small proteins to atomic resolutions. However, predicting structures for proteins larger than 150 residues still remains a challenge, with bottlenecks from both force field and conformational search.