Publications

2020

Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase
Lisa Ngu, Jenifer N. Winters, Kien Nguyen, Kevin E. Ramos, Nicholas A. DeLateur, Lee Makowski, Paul C. Whitford, Mary Jo Ondrechen, Penny J. Beuning, PLoS ONE 15(2): e0228487

2019

Tri-arginine exosite patch of caspase-6 recruits substrates for hydrolysis
Derek J. MacPherson, Caitlyn L. Mills, Mary Jo Ondrechen, and Jeanne A. Hardy, Biol. Chem. 294(1), 71-88
Synthesis of Benzoylbenzamide Derivatives of 17α-E-Vinyl Estradiol and Evaluation as Ligands for the Estrogen Receptor-α Ligand Binding Domain
Robert N. Hanson, Emmett McCaskill, Edward Hua, Pakamas Tongcharoensirikul, Robert Dilis, Jessa L. Silver, Timothy A. Coulther, Mary Jo Ondrechen, David Labaree, and Richard B. Hochberg, Steroids 144, 15-20

2018

Prediction of active site and distal residues in coli DNA polymerase III alpha polymerase activity
Ramya Parasuram, Timothy A. Coulther, Judith M. Hollander, Elise Keston-Smith, Mary Jo Ondrechen, Penny J. Beuning, Biochemistry 57(7), 1063-1072
PMID: 29341605
In vitro and in vivo evaluation of C-11-labeled azetidine-carboxylates for imaging monoacylglycerol lipase by PET imaging studies
Ran Cheng, Wakana Mori, Longle Ma, Mireille Alhouayek, Akiko Hatori, Yiding Zhang, Daisuke Ogasawara, Gengyang Yuan, Zhen Chen, Xiaofei Zhang, Hang Shi, Tomoteru Yamasaki, Lin Xie, Katsushi Kumata, Masayuki Fujinaga, Yuji Nagai, Takafumi Minamimoto, Mona Svensson, Lu Wang, Yunfei Du, Mary Jo Ondrechen, Neil Vasdev, Benjamin Cravatt, Christopher Fowler, Ming-Rong Zhang and Steven H. Liang, Med. Chem. 61, 2278-2291
PMID: 29481079
Functional classification of protein structures by local structure matching in graph representation
Caitlyn L. Mills, Rohan Garg, Joslynn S. Lee, Liang Tian, Alexandru Suciu, Gene Cooperman, Penny J. Beuning, Mary Jo Ondrechen, Protein Science 27, 1125-1135 (2018)
PMID: 29604149
A Practical Synthesis of Glycinamide Ribonucleotide
Debarpita Ray, Penny J. Beuning, Mary Jo Ondrechen, and George A. O’Doherty Heterocycles, published online
DOI: 10.3987/COM-18-S(T)50

2017

Fluorinated adenosine A2A receptor antagonists inspired by Preladenant as potential cancer immunotherapeutics
Gengyang Yuan, Tanner C. Jankins, Christopher G. Patrick Jr., Phaethon Philbrook, Olivia Sears, Stephen Hatfield, Michail Sitkovsky, Neil Vasdev, Steven H. Liang, Mary Jo Ondrechen, Michael P. Pollastri, Graham B. Jones, J. Med. Chem.
PMID: 29201461
Homology Modeling Inspired Synthesis of 5-HT2A Receptor Inhibitors: A Diazepine Analogue of the Atypical Antipsychotic JL13
Enrico Mongeau, Gengyang Yuan, Zachary Minden, Scott Waldron, Raymond Booth, Daniel Felsing, Mary Jo Ondrechen, and Graham B. Jones, Central Nervous System Agents in Medicinal Chemistry 17(3), 239-244
PMID: 28462720

2016

Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases
Ramya Parasuram, Caitlyn L. Mills, Zhouxi Wang, Saroja Somasundaram, Penny J. Beuning, Mary Jo Ondrechen, Methods 93, 51-63
PMID: 26564235

2015

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
PMID: 25637676
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
PMID: 25848497
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
PMID: 25627867

2014

American Indian Science and Engineering Society (AISES): Building a Successful Model for Diversity and Inclusion
Mary Jo Ondrechen in Career Challenges and Opportunities in the Global Chemistry Enterprise, ACS Symposium Series 1169, edited by N. Cheng, Sadiq Shah, and Marinda Li Wu, Oxford University Press

2013

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, 62, 777-784
PMID: 22889561

Protein Function Annotation with Structurally Aligned Local Sites of Activity (SALSAs)
Zhouxi Wang, Pengcheng Yin, Joslynn S. Lee, Ramya Parasuram, Srinivas Somarowthu, and Mary Jo Ondrechen, BMC Bioinformatics, 14 (Suppl 3):S13
PMID: 23514271
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
PMID: 24126093

2012

POOL server: Machine learning application for functional site prediction in proteins
Srinivas Somarowthu and Mary Jo Ondrechen, Bioinformatics 28 (15), 2078-2079
PMID: 22661648
Effects of non-catalytic, distal amino acid residues on activity of coli DinB (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
PMID: 23034734

2011

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
PMID: 21254002
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
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
PMID: 21538547
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
PMID: 21473592
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
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, Medicinal Chemistry 54 (23), 8188-8194
PMID: 22023548

2010

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
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

2009

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
PMID: 19148270

2008

Enhanced Sensitivity in Prediction of Protein Active Sites with THEMATICS and Support Vector Machines
W. Tong, Y. Wei, L.F. Murga, J. Ko, M.J. Ondrechen, and R. J. Williams, Protein Science 17, 333-341
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
Identification of a twin-arginine leader peptide binding site in DmsD; Defined through random and bioinformatics-directed mutagenesis
C.S. Chan, T.M.L. Winstone, L. Chang, H. Li, C. Stevens, M.L. Workentine, Y. Wei, M.J. Ondrechen, M. Paetzel, and R.J. Turner, Biochemistry 47, 2749-2759
PMID: 18247574
pH-dependent Interdomain Tethers of CD1b Regulate Its Antigen Capture
M. Relloso, T.-Y. Cheng, J.S. Im, E. Parisini, C. Roura-Mir, C. DeBono, D. M. Zajonc, L. F. Murga, M.J. Ondrechen, I.A. Wilson, S.A. Porcelli, and D.B. Moody, Immunity 28, 774-786
PMID: 18538591

2007

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
PMID: 17257049
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
PMID: 17419878
Computed Protonation Properties: Unique Capabilities for Protein Functional Site Prediction
F. Murga, Y. Wei, and M.J. Ondrechen, Genome Informatics 19, 107-118
PMID: 18546509

2005

Active Site Prediction for Comparative Model Structures with THEMATICS
I.A. Shehadi, A. Abyzov, A. Uzun, Y. Wei, L.F. Murga, V. Ilyin, and M.J. Ondrechen, Journal of Bioinformatics and Computational Biology 3, 127-143
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
Prediction of Active Sites for Protein Structures from Computed Chemical Properties
J. Ko, L.F. Murga, Y.Wei, and M.J. Ondrechen, Bioinformatics 21, i258-i265
Central Moments Based Statistical Analysis for the Determination of Functional Sites in Proteins with THEMATICS
L.F. Murga, J. Ko, Y. Wei, and M.J. Ondrechen, in Bioinformatics of Genome Regulation and Structure II, N. Kolchanov and R. Hofestaedt, Eds., Springer Science & Business Media, Inc, pp 215-224

2004

THEMATICS is Effective for Active Site Prediction in Comparative Model Structures
I.A. Shehadi, A. Uzun, L.F. Murga, V. Ilyin and M.J. Ondrechen, Conferences in Research and Practice in Information Technology, Vol. 29, Yi-Ping Phoebe Chen, Editor, 209-215
Protein Structure to Function: Insights from Computation
D. Ringe, Y. Wei, K.R. Boino and M.J. Ondrechen,Cellular and Molecular Life Sciences 61, 387-392
Identifying Functional Sites Based on Prediction of Charge Group Behavior
M.J. Ondrechen, Protocols in Bioinformatics, A.D. Baxevanis, et al., Editors, John Wiley & Sons: Hoboken, N.J. p. 8.6.1 – 8.6.10
Statistical Metrics for Protein Active Site Prediction with THEMATICS
J. Ko, P. Andre, L.F. Murga and M.J. Ondrechen, Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure BGRS, 1, 282-285, Novosibirsk, Russia

2003

Prediction of Protein Function with THEMATICS
M.J. Ondrechen, L.F. Murga, J.G. Clifton and D. Ringe, Currents in Computational Molecular Biology, 21-22

2002

Future Directions in Protein Function Prediction
I.A. Shehadi, H. Yang and M.J. Ondrechen, Molecular Biology Reports 29, 329-335
THEMATICS as a Tool for Functional Genomics
M.J. Ondrechen, Genome Informatics 13, 563-564

2001

A Model for Enzyme-Substrate Interaction in Alanine Racemase
M.J. Ondrechen, J.M. Briggs and J.A. McCammon, Journal of the American Chemical Society 123, 2830-2834
PMID: 11456969
THEMATICS: A Simple Computational Predictor of Enzyme Function from StructureM.J. Ondrechen, J.G. Clifton & D. Ringe, Nat. Acad. Sci. USA 98, 12473-12478
PMID: 11606719