Future directions in protein function prediction

• Published in: Molecular biology reports Vol. 29; no. 4; pp. 329 - 335
• Main Authors: Shehadi, Ihsan A., Yang, Huyuan, Ondrechen, Mary Jo
• Format: Journal Article
• Language: English
• Published: Netherlands Springer Nature B.V 01.12.2002
• Subjects: Adenosine Kinase - chemistry; Adenosine Kinase - metabolism; Binding Sites; Computational Biology - methods; Computational Biology - trends; DNA-(Apurinic or Apyrimidinic Site) Lyase - chemistry; DNA-(Apurinic or Apyrimidinic Site) Lyase - metabolism; HIV Protease - chemistry; HIV Protease - metabolism; Humans; Hydrogen-Ion Concentration; Kinases; Kinetics; Proteins - chemistry; Proteins - metabolism; Proteomics - trends; Structure-Activity Relationship; Titrimetry
• ISSN: 0301-4851; 1573-4978
• DOI: 10.1023/A:1021220208562

New directions in computational methods for the prediction of protein function are discussed. THEMATICS, a method for the location and characterization of the active sites of enzymes, is featured. THEMATICS, for Theoretical Microscopic Titration Curves, is based on well-established finite-difference Poisson-Boltzmann methods for computing the electric field function of a protein. THEMATICS requires only the structure of the subject protein and thus may be applied to proteins that bear no similarity in structure or sequence to any previously characterized protein. The unique features of catalytic sites in proteins are discussed. Discussion of the chemical basis for the predictive powers of THEMATICS is featured in this paper. Some results are given for three illustrative examples: HIV-1 protease, human apurinic/apyrimidinic endonuclease, and human adenosine kinase.