Future directions in protein function prediction.
作者： Ihsan A. Shehadi , Huyuan Yang , Mary Jo Ondrechen
关键词:
摘要: New directions in computational methods for the prediction of protein function are discussed. THEMATICS, a method location and characterization active sites enzymes, is featured. Theoretical Microscopic Titration Curves, based on well-established finite-difference Poisson-Boltzmann computing electric field protein. THEMATICS requires only structure subject thus may be applied to proteins that bear no similarity or sequence any previously characterized The unique features catalytic Discussion chemical basis predictive powers featured this paper. Some results given three illustrative examples: HIV-1 protease, human apurinic/apyrimidinic endonuclease, adenosine kinase.
springer.com
sci-hub.se 参考文章(51)
Edward M. Marcotte, Matteo Pellegrini, Michael J. Thompson, Todd O. Yeates, David Eisenberg, A combined algorithm for genome-wide prediction of protein function Nature. ,vol. 402, pp. 83- 86 ,(1999) , 10.1038/47048
Patricia C. Babbitt, Teri E. Klein, Superfamily Analysis: Understanding Protein Function from Structure and Sequence Encyclopedia of Computational Chemistry. ,(2002) , 10.1002/0470845015.CPA030
Jacquelyn S. Fetrow, Naomi Siew, Jeffrey Skolnick, Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily The FASEB Journal. ,vol. 13, pp. 1866- 1874 ,(1999) , 10.1096/FASEBJ.13.13.1866
Stephen K Burley, Steven C Almo, Jeffrey B Bonanno, Malcolm Capel, Mark R Chance, Terry Gaasterland, Dawei Lin, Andrej Šali, F. William Studier, Subramanyam Swaminathan, Structural genomics: beyond the human genome project. Nature Genetics. ,vol. 23, pp. 151- 157 ,(1999) , 10.1038/13783
Connie M. Oshiro, Irwin D. Kuntz, Ronald M. A. Knegtel, Molecular Docking and Structure‐based Design John Wiley & Sons, Ltd. pp. 1- 23 ,(2002) , 10.1002/0470845015.CMA020M
E.E. Rutenber, E.B. Fauman, R.J. Keenan, R.M. Stroud, Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design. Journal of Biological Chemistry. ,vol. 268, pp. 15343- 15346 ,(1997) , 10.2210/PDB2AID/PDB
Adrian H Elcock, Prediction of functionally important residues based solely on the computed energetics of protein structure Journal of Molecular Biology. ,vol. 312, pp. 885- 896 ,(2001) , 10.1006/JMBI.2001.5009
Clifford D. Mol, Tadahide Izumi, Sankar Mitra, John A. Tainer, DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination Nature. ,vol. 403, pp. 451- 456 ,(2000) , 10.1038/35000249
Lam H Nguyen, Daniel Barsky, Jan P Erzberger, David M Wilson, Mapping the protein-DNA interface and the metal-binding site of the major human apurinic/apyrimidinic endonuclease. Journal of Molecular Biology. ,vol. 298, pp. 447- 459 ,(2000) , 10.1006/JMBI.2000.3653
Jason S. Bardi, Irene Luque, Ernesto Freire, Structure-Based Thermodynamic Analysis of HIV-1 Protease Inhibitors† Biochemistry. ,vol. 36, pp. 6588- 6596 ,(1997) , 10.1021/BI9701742