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Bioinformatics. 2007 Sep 1;23(17):2203-9. Epub 2007 Jun 22.

Interaction-site prediction for protein complexes: a critical assessment.

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Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.



Proteins function through interactions with other proteins and biomolecules. Protein-protein interfaces hold key information toward molecular understanding of protein function. In the past few years, there have been intensive efforts in developing methods for predicting protein interface residues. A review that presents the current status of interface prediction and an overview of its applications and project future developments is in order.


Interface prediction methods rely on a wide range of sequence, structural and physical attributes that distinguish interface residues from non-interface surface residues. The input data are manipulated into either a numerical value or a probability representing the potential for a residue to be inside a protein interface. Predictions are now satisfactory for complex-forming proteins that are well represented in the Protein Data Bank, but less so for under-represented ones. Future developments will be directed at tackling problems such as building structural models for multi-component structural complexes.

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