Future directions in protein function prediction.
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.
Shehadi
Ihsan A
IA
Department of Chemistry, United Arab Emirates University, Al-Ain, United Arab Emirates.
Yang
Huyuan
H
Ondrechen
Mary Jo
MJ
D000248:Adenosine Kinase / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods* / Q000639:trends*; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000737:chemistry / Q000378:metabolism; D016333:HIV Protease / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics / Q000639:trends; D013329:Structure-Activity Relationship; D017186:Titrimetry
D011506:Proteins; D000248:Adenosine Kinase; D016333:HIV Protease; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase