Prediction of protein structural similarities using a 3D-1D compatibility method

Yo Matsuo (
Ken Nishikawa (

Protein Engineering Research Institute,
6-2-3 Furuedai, Suita, Osaka 565, Japan.


The 3D-1D compatibility method is a new approach to protein structure prediction. It evaluates the compatibility of a one-dimensional (1D) amino acid sequence with known three-dimensional (3D) structures, and select the most likely structure. We have developed a method, which evaluates the 3D-1D compatibility using the following functions: side-chain packing, solvation, hydrogen-bonding, and local conformation functions. The method has been applied to a large number of sequences in databases. Here, the predictions of the structural similarities between the following pairs are described in detail: spermidine/putrescine-binding protein and maltose-binding protein, shikimate kinase and adenylate kinase, and mannose permease hydrophilic subunit (IIAB^{Man}) and galactose/glucose-binding protein. Functional and evolutionary implications of the predictions are discussed. Through these examples of predictions, the present work demonstrates the promise of the 3D-1D method.