Some Recent Publications

22.   “Prediction of distal residue participation in enzyme catalysis,” Heather R. Brodkin, Nicholas A. DeLateur, Srinivas Somarowthu, Caitlyn L. Mills, Walter R. Novak, Penny J. Beuning, Dagmar Ringe, Mary Jo Ondrechen, Protein Science 24 (5), 762-778 (2015).

21.  “Biochemical Functional Predictions for Protein Structures of Unknown or Uncertain Function,” Caitlyn L. Mills, Penny J. Beuning, Mary Jo Ondrechen, Computational and Structural Biotechnology Journal 13, 182-191 (2015).

20.  “Synthesis and evaluation of 2-halogenated-1,1-bis(4-hydroxyphenyl)-2-(3-hydroxyphenyl)-ethylenes as potential estrogen receptor-targeted radiodiagnostic and radiotherapeutic agents,” Robert N. Hanson, Pakamas Tongcharoensirikul, Kelton Barnsley, Mary Jo Ondrechen, Alun Hughes, Eugene R. DeSombre, Steroids 96, 50-62 (2015).

19. “Design and evaluation of xanthine based adenosine receptor antagonists: Potential hypoxia targeted immunotherapies,” R. Thomas, J. Lee, V. Chevalier, S. Sadler, K. Selesniemi, S. Hatfield, M. Sitkovsky, M.J. Ondrechen, and G.B. Jones, Bioorganic and Medicinal Chemistry 21, 7453-7464 (2013). (Contact us for reprint)

18. “Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs),” Zhouxi Wang, Pengcheng Yin, Joslynn S Lee, Ramya Parasuram, Srinivas Somarowthu, Mary Jo Ondrechen, BMC Bioinformatics, 2013, 14(Suppl 3):S13.

17. “Effects of non-catalytic, distal amino acid residues on activity of E. coliDinB (DNA Polymerase IV),” Jason M. Walsh, Ramya Parasuram, Pradyumna R. Rajput, Eriks Rozners, Mary Jo Ondrechen, and Penny J. Beuning, Environmental and Molecular Mutagenesis 53(9), 766-776 (2013).  (Contact us for a reprint)

16. “The human Aurora kinase inhibitor danusertib is a lead compound for anti-trypanosomal drug discovery via target repurposing,” Stefan O. Ochiana, Vidya Pandarinath, Zhouxi Wang, Rishika Kapoor, Mary Jo Ondrechen, Larry Ruben, and Michael P. Pollastri, European Journal Medicinal Chemistry, (2012). (PMID: 22889561) (Contact us for a preprint)

15. “POOL server: Machine learning application for functional site prediction in proteins,” Srinivas Somarowthu and Mary Jo Ondrechen, Bioinformatics 28(15), 2078-2079 (2012).

14. “Pharmacological Validation of Trypanosoma brucei Phosphodiesterases B1 and B2 as Druggable Targets for African Sleeping Sickness,” Nicholas D. Bland, Cuihua Wang, Craig Tallman, Alden E. Gustafson, Zhouxi Wang, Trent D. Ashton, Stefan Ochiana, Gregory McAllister, Kristina Cotter, Anna P. Fang, Lara Gechijian, Norman Garceau, Rajiv Gangurde, Ron Ortenberg, Mary Jo Ondrechen, Robert K. Campbell, and Michael P. Pollastri, J. Medicinal Chemistry, 54(23) 8188-8194 (2011). PMID:22023548  (Contact us for a pdf version)

13. “A Tale of Two Isomerases: Compact versus Extended Active Sites in Ketosteroid Isomerase and Phosphoglucose Isomerase,” Srinivas Somarowthu, Heather R. Brodkin, J. Alejandro D’Aquino, Dagmar Ringe, Mary Jo Ondrechen*, and Penny J. Beuning*, Biochemistry 50(43) 9283-9295 (2011). (Contact us for a pdf version)

12. “High Performance Prediction of Functional Residues in Proteins with Machine Learning and Computed Input Features,” S. Somarowthu, H. Yang, D.G.C. Hildebrand, and M.J. Ondrechen, Biopolymers 95(6), 390-400 (2011). (Contact us for a pdf version)

11. “Electrostatic Properties for Protein Functional Site Prediction,” J.S. Lee and M.J.Ondrechen, in Protein Function Prediction for Omics Era, D. Kihara, Ed., Springer, Dordrecht, pp. 183-196 (2011). (Contact us for a pdf version)

10. “Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity,” G.W. Han, J. Ko, C.L. Farr, M.C. Deller, Q. Xu, H.-J. Chiu, M.D. Miller, J. Sefcikova, S. Somarowthu, P.J. Beuning, M.-A.´ Elsliger, A.M. Deacon, A. Godzik, S.A. Lesley, I.A. Wilson,* and M.J. Ondrechen*, Proteins 79(7), 2146-2160 (2011). (Contact us for a pdf version)

9. “Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida,” Heather R. Brodkin, Walter R. P. Novak, Amy C. Milne, J. Alejandro D’Aquino, N. M. Karabacak, Ilana G. Goldberg, Jeffrey N. Agar, Mark S. Payne, Gregory A. Petsko, Mary Jo Ondrechen, Dagmar Ringe, Biochemistry 50(22), 4923-4935 (2011). (Contact us for a pdf version)

8. “Functional Classification of Protein 3D Structures from Predicted Local Interaction Sites,” R. Parasuram, J.S. Lee, P. Yin, S. Somarowthu, M.J. Ondrechen, Journal of Bioinformatics and Computational Biology, 8, 1-15 (2010).

7. “High Conservation of Amino Acids with Anomalous Protonation Behavior,” D.G.C. Hildebrand, H. Yang, M.J. Ondrechen, and R.J. Williams, Current Bioinformatics, 5(2), 134-140 (2010). Please contact us for a pdf reprint.

6. “Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Active Site Residues Using 3D Structure and Sequence Properties,” W. Tong, Y. Wei, L.F. Murga, M.J. Ondrechen, and R.J. Williams, PLoS Computational Biology, 5(1): e1000266 (2009)

5. “Prediction of Interaction Sites from Apo 3D Structures When the Holo Conformation is Different,” L.F. Murga, M.J. Ondrechen, and D. Ringe, Proteins: Structure Function Bioinformatics 72:3, 980-992 (2008). Please contact us for a pdf reprint

4. “Selective Prediction of Interaction Sites in Protein Structures with THEMATICS,” Y. Wei, J. Ko, L.F. Murga, and M.J. Ondrechen, BMC Bioinformatics 8:119, (2007)

3. “Identification of Functional Subclasses in the DJ-1 Superfamily Proteins,” Y. Wei, D. Ringe, M.A. Wilson, and M.J. Ondrechen, PloS Computational Biology 3, e10, 120-126 (2007)

2. “Statistical Criteria for Protein Active Site Prediction with THEMATICS,” J. Ko, L.F. Murga, P. Andre, H. Yang, M.J. Ondrechen, R.J. Williams, A. Agunwamba, and D.E. Budil, Proteins: Structure Function Bioinformatics 59, 183-195 (2005)

1. “THEMATICS: A Simple Computational Predictor of Enzyme Function from Structure,” M.J. Ondrechen, J.G. Clifton & D. Ringe, Proc. Nat. Acad. Sci. USA 98, 12473-12478 (2001)