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Curr Opin Struct Biol. 2008 Jun;18(3):342-8. doi: 10.1016/j.sbi.2008.02.004. Epub 2008 Apr 22.

Progress and challenges in protein structure prediction.

Author information

  • Center for Bioinformatics and Department of Molecular Biosciences, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, United States. yzhang@ku.edu


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.

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