All Stories

  1. Distal residues contribute to enzymatic catalysis in human phosphoglucose isomerase through modulation of dynamics and electrostatics

    Article • The Journal of Chemical Physics, July 2025, American Institute of Physics

    Mary Ondrechen

  2. Cartilage targeting cationic peptide carriers display deep cartilage penetration and retention in a rabbit model of post-traumatic osteoarthritis

    Article • Osteoarthritis and Cartilage, June 2025, Elsevier

    Mary Ondrechen

  3. Biochemical Characterization of Disease-Associated Variants of Human Ornithine Transcarbamylase

    Article • ACS Chemical Biology, March 2025, American Chemical Society (ACS)

    Mary Ondrechen

  4. Revisiting the Roles of Catalytic Residues in Human Ornithine Transcarbamylase

    Article • Biochemistry, June 2024, American Chemical Society (ACS)

    Mary Ondrechen

  5. Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS

    Article • PLoS Biology, January 2024, PLOS

    Mary Ondrechen

  6. Biochemical Activity of 17 Cancer-Associated Variants of DNA Polymerase Kappa Predicted by Electrostatic Properties

    Article • Chemical Research in Toxicology, October 2023, American Chemical Society (ACS)

    Mary Ondrechen

  7. Functional annotation of haloacid dehalogenase superfamily structural genomics proteins

    Article • Biochemical Journal, October 2023, Portland Press Ltd.

    Mary Ondrechen

  8. Hydration sphere structure of architectural molecules: Polyethylene glycol and polyoxymethylene oligomers

    Article • Journal of Molecular Liquids, August 2023, Elsevier

    Mary Ondrechen

  9. Enzyme active sites: Identification and prediction of function using computational chemistry

    Article • Current Opinion in Structural Biology, June 2022, Elsevier

    Mary Ondrechen

  10. Stereoselective Synthesis of β-Glycinamide Ribonucleotide

    Article • Molecules, April 2022, MDPI AG

    Mary Ondrechen

  11. Electrostatic fingerprints of catalytically active amino acids in enzymes

    Article • Protein Science, April 2022, Wiley

    Mary Ondrechen

  12. Functional Characterization of Structural Genomics Proteins in the Crotonase Superfamily

    Article • ACS Chemical Biology, January 2022, American Chemical Society (ACS)

    Mary Ondrechen

  13. Best Practices to Diversify Chemistry Faculty

    Article • Journal of Chemical Education, November 2021, American Chemical Society (ACS)

    Mary Ondrechen

  14. Design, synthesis, and characterization of [ 18 F]mG2P026 as a high contrast PET imaging ligand for metabotropic glutamate receptor 2

    Article • July 2021, openRxiv

    Mary Ondrechen

  15. Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase

    Article • Protein Science, May 2021, Wiley

    Mary Ondrechen

  16. Amino acid interactions that facilitate enzyme catalysis

    Article • The Journal of Chemical Physics, May 2021, American Institute of Physics

    Mary Ondrechen

  17. Design, Synthesis, and Characterization of Benzimidazole Derivatives as Positron Emission Tomography Imaging Ligands for Metabotropic Glutamate Receptor 2

    Article • Journal of Medicinal Chemistry, September 2020, American Chemical Society (ACS)

    Mary Ondrechen

  18. Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase

    Article • PLOS One, February 2020, PLOS

    Mary Ondrechen

  19. Tri-arginine exosite patch of caspase-6 recruits substrates for hydrolysis

    Article • Journal of Biological Chemistry, January 2019, Elsevier

    Mary Ondrechen

  20. Prediction of Active Site and Distal Residues in E. coli DNA Polymerase III alpha Polymerase Activity

    Article • Biochemistry, January 2018, American Chemical Society (ACS)

    Mary Ondrechen

  21. Homology Modeling Inspired Synthesis of 5-HT2A Receptor Inhibitors: A Diazepine Analogue of the Atypical Antipsychotic JL13

    Article • Central Nervous System Agents in Medicinal Chemistry, October 2017, Bentham Science Publishers

    Mary Ondrechen

  22. Fluorinated Adenosine A2AReceptor Antagonists Inspired by Preladenant as Potential Cancer Immunotherapeutics

    Article • International Journal of Medicinal Chemistry, January 2017, Hindawi Publishing Corporation

    Mary Ondrechen

  23. Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases

    Article • Methods, January 2016, Elsevier

    Mary Ondrechen

  24. Prediction of distal residue participation in enzyme catalysis

    Article • Protein Science, April 2015, Wiley

    Mary Ondrechen

  25. Synthesis and evaluation of 2-halogenated-1,1-bis(4-hydroxyphenyl)-2-(3-hydroxyphenyl)-ethylenes as potential estrogen receptor-targeted radiodiagnostic and radiotherapeutic agents

    Article • Steroids, April 2015, Elsevier

    Mary Ondrechen

  26. Biochemical functional predictions for protein structures of unknown or uncertain function

    Article • Computational and Structural Biotechnology Journal, January 2015, American Association for the Advancement of Science

    Mary Ondrechen

  27. American Indian Science and Engineering Society (AISES): Building a Successful Model for Diversity and Inclusion

    Article • January 2014, American Chemical Society (ACS)

    Mary Ondrechen

  28. Design and evaluation of xanthine based adenosine receptor antagonists: Potential hypoxia targeted immunotherapies

    Article • Bioorganic & Medicinal Chemistry, December 2013, Elsevier

    Mary Ondrechen

  29. The human Aurora kinase inhibitor danusertib is a lead compound for anti-trypanosomal drug discovery via target repurposing

    Article • European Journal of Medicinal Chemistry, April 2013, Elsevier

    Mary Ondrechen

  30. Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs)

    Article • BMC Bioinformatics, February 2013, Springer Science + Business Media

    Mary Ondrechen

  31. Effects of non‐catalytic, distal amino acid residues on activity of E. coli DinB (DNA polymerase IV)

    Article • Environmental and Molecular Mutagenesis, October 2012, Wiley

    Mary Ondrechen

  32. POOL server: machine learning application for functional site prediction in proteins

    Article • Bioinformatics, June 2012, Oxford University Press (OUP)

    Mary Ondrechen

  33. Pharmacological Validation of Trypanosoma brucei Phosphodiesterases B1 and B2 as Druggable Targets for African Sleeping Sickness

    Article • Journal of Medicinal Chemistry, November 2011, American Chemical Society (ACS)

    Mary Ondrechen

  34. A Tale of Two Isomerases: Compact versus Extended Active Sites in Ketosteroid Isomerase and Phosphoglucose Isomerase

    Article • Biochemistry, October 2011, American Chemical Society (ACS)

    Mary Ondrechen

  35. Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida

    Article • Biochemistry, May 2011, American Chemical Society (ACS)

    Mary Ondrechen

  36. Crystal structure of a metal‐dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity

    Article • Proteins Structure Function and Bioinformatics, May 2011, Wiley

    Mary Ondrechen

  37. High‐performance prediction of functional residues in proteins with machine learning and computed input features

    Article • Biopolymers, January 2011, Wiley

    Mary Ondrechen

  38. FUNCTIONAL CLASSIFICATION OF PROTEIN 3D STRUCTURES FROM PREDICTED LOCAL INTERACTION SITES

    Article • Journal of Bioinformatics and Computational Biology, December 2010, World Scientific Pub Co Pte Lt

    Mary Ondrechen

  39. High Conservation of Amino Acids with Anomalous Protonation Behavior

    Article • Current Bioinformatics, June 2010, Bentham Science Publishers

    Mary Ondrechen

  40. Models for the spectra of bridged mixed-valence dimers

    Article • International Journal of Quantum Chemistry, June 2009, Wiley

    Mary Ondrechen

  41. Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties

    Article • PLoS Computational Biology, January 2009, PLOS

    Mary Ondrechen

  42. pH-Dependent Interdomain Tethers of CD1b Regulate Its Antigen Capture

    Article • Immunity, June 2008, Elsevier

    Dirk Zajonc, Mary Ondrechen

  43. Prediction of interaction sites from apo 3D structures when the holo conformation is different

    Article • Proteins Structure Function and Bioinformatics, February 2008, Wiley

    Mary Ondrechen

  44. Identification of Residues in DmsD for Twin-Arginine Leader Peptide Binding, Defined through Random and Bioinformatics-Directed Mutagenesis

    Article • Biochemistry, February 2008, American Chemical Society (ACS)

    Professor Raymond J. Turner, Mary Ondrechen

  45. Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines

    Article • Protein Science, February 2008, Wiley

    Mary Ondrechen

  46. Selective prediction of interaction sites in protein structures with THEMATICS

    Article • BMC Bioinformatics, April 2007, Springer Science + Business Media

    Mary Ondrechen

  47. Identification of Functional Subclasses in the DJ-1 Superfamily Proteins

    Article • PLoS Computational Biology, January 2007, PLOS

    Mary Ondrechen

  48. Prediction of active sites for protein structures from computed chemical properties

    Article • Bioinformatics, June 2005, Oxford University Press (OUP)

    Mary Ondrechen

  49. Statistical criteria for the identification of protein active sites using theoretical microscopic titration curves

    Article • Proteins Structure Function and Bioinformatics, February 2005, Wiley

    Mary Ondrechen

  50. ACTIVE SITE PREDICTION FOR COMPARATIVE MODEL STRUCTURES WITH THEMATICS

    Article • Journal of Bioinformatics and Computational Biology, February 2005, World Scientific Pub Co Pte Lt

    Mary Ondrechen

  51. Physicochemical Methods for Prediction of Functional Information for Proteins

    Article • Israel Journal of Chemistry, October 2004, Wiley

    Mary Ondrechen

  52. Protein structure to function: insights from computation

    Article • Cellular and Molecular Life Sciences, February 2004, Springer Science + Business Media

    Mary Ondrechen

  53. Future directions in protein function prediction

    Article • Molecular Biology Reports, December 2002, Springer Science + Business Media

    Mary Ondrechen

  54. THEMATICS: A simple computational predictor of enzyme function from structure

    Article • Proceedings of the National Academy of Sciences, October 2001, Proceedings of the National Academy of Sciences

    Mary Ondrechen

  55. A Model for Enzyme−Substrate Interaction in Alanine Racemase

    Article • Journal of the American Chemical Society, March 2001, American Chemical Society (ACS)

    Mary Ondrechen

  56. Theory of Electroabsorption Spectroscopy in Pyrazine-Bridged Ru Dimers

    Article • Journal of the American Chemical Society, March 1999, American Chemical Society (ACS)

    Mary Ondrechen

  57. Theory of the Stark Effect in protein systems containing an electron donor–acceptor couple

    Article • Journal of Inorganic Biochemistry, July 1998, Elsevier

    Mary Ondrechen

  58. Theory of the Stark Effect spectral lineshape for a delocalized mixed-valence complex

    Article • Inorganic Chemistry Communications, April 1998, Elsevier

    Mary Ondrechen

  59. Role of vibronic coupling and correlation effects on the optical properties of mixed-valent and monovalent dimer compounds: the Creutz-Taube ion and its monovalent analogs

    Article • The Journal of Physical Chemistry, June 1995, American Chemical Society (ACS)

    Mary Ondrechen

  60. Electron donor-acceptor couples

    Article • International Reviews in Physical Chemistry, March 1995, Taylor & Francis

    Mary Ondrechen

  61. Potential energy surfaces for a mixed-valence dimer in an applied electric field

    Article • Theoretica Chimica Acta, March 1995, Springer Science + Business Media

    Mary Ondrechen

  62. The electronic structure of pentaammine(pyrazine) ruthenium(II) and (III): the metal-ligand π conjugation and its implications in electron delocalization

    Article • Inorganica Chimica Acta, November 1994, Elsevier

    Mary Ondrechen

  63. Comment on the Calculation of Absorption Line Shapes for Mixed-Valence Dimers

    Article • The Journal of Physical Chemistry, October 1994, American Chemical Society (ACS)

    Mary Ondrechen

  64. Third-order nonlinear optical properties of finite bridged polymers

    Article • Chemical Physics Letters, April 1993, Elsevier

    Mary Ondrechen

  65. An electronic mechanism for electron pairing in antiferromagnetic bridged mixed-valence systems

    Article • The Journal of Chemical Physics, February 1992, American Institute of Physics

    Mary Ondrechen

  66. A hybrid hubbard model for discrete and periodic backbonded complexes

    Article • Chemical Physics Letters, January 1990, Elsevier

    Mary Ondrechen

  67. Nonadiabatic quantum mechanical treatment of the absorption lineshape of bridged mixed-valence dimers

    Article • The Journal of Physical Chemistry, April 1989, American Chemical Society (ACS)

    Mary Ondrechen

  68. A model for the optical absorption spectrum of (.mu.-pyrazine) decaamminediruthenium(5+): What hath Creutz and Taube wrought?

    Article • Journal of the American Chemical Society, March 1987, American Chemical Society (ACS)

    Mary Ondrechen

  69. Electronic structure of the Creutz-Taube ion

    Article • Journal of the American Chemical Society, March 1987, American Chemical Society (ACS)

    Mary Ondrechen

  70. An analysis of the absorption and fluorescence spectra of trimethylamine. Determination of the ~A-~X origin and the ground state inversion barrier

    Article • Journal of the American Chemical Society, July 1986, American Chemical Society (ACS)

    Mary Ondrechen

  71. Creutz-Taube ion: a model for the EPR g tensor which includes the bridging ligand

    Article • Journal of the American Chemical Society, April 1986, American Chemical Society (ACS)

    Mary Ondrechen

  72. Line shape of the intervalence transfer band in bridged mixed-valence dimers: the delocalized case

    Article • Journal of the American Chemical Society, October 1985, American Chemical Society (ACS)

    Mary Ondrechen

  73. A model for the intervalence transfer band profile of bridged mixed-valence dimers

    Article • Chemical Physics Letters, December 1984, Elsevier

    Mary Ondrechen

  74. Two-dimensional potential surfaces for bridged mixed-valence dimers

    Article • The Journal of Physical Chemistry, November 1984, American Chemical Society (ACS)

    Mary Ondrechen

  75. The electronic structure of the creutz-taube ion: A hartree-fock-slater study

    Article • Chemical Physics Letters, August 1984, Elsevier

    Mary Ondrechen

  76. Thermodynamics for processes in finite time

    Article • Accounts of Chemical Research, August 1984, American Chemical Society (ACS)

    Mary Ondrechen

  77. The generalized Carnot cycle: A working fluid operating in finite time between finite heat sources and sinks

    Article • The Journal of Chemical Physics, April 1983, American Institute of Physics

    Mary Ondrechen

  78. Adiabatic potentials for a bridged three-site electron-transfer system

    Article • Chemical Physics Letters, December 1982, Elsevier

    Mary Ondrechen

  79. Through-bridge electron transfer: A propagator study of a simple three-site model

    Article • Chemical Physics Letters, May 1982, Elsevier

    Mary Ondrechen

  80. Energetics and dynamics of large Van der Waals molecules

    Article • Faraday Discussions of the Chemical Society, January 1982, Royal Society of Chemistry

    Mary Ondrechen

  81. Maximum work from a finite reservoir by sequential Carnot cycles

    Article • American Journal of Physics, July 1981, American Association of Physics Teachers (AAPT)

    Mary Ondrechen

  82. Hexaammineruthenium(II,III) and pentaamminedinitrogenruthenium(II). A Hartree-Fock-Slater study

    Article • Journal of the American Chemical Society, April 1981, American Chemical Society (ACS)

    Mary Ondrechen

  83. Thermodynamics in finite time: Processes with temperature-dependent chemical reactions

    Article • The Journal of Chemical Physics, December 1980, American Institute of Physics

    Mary Ondrechen

  84. Thermodynamics in finite time: A chemically driven engine

    Article • The Journal of Chemical Physics, May 1980, American Institute of Physics

    Mary Ondrechen

  85. Effect of basis function overlap on intramolecular electron transfer amplitudes: some results for a two-site hubbard model

    Article • Chemical Physics Letters, November 1977, Elsevier

    Mary Ondrechen

  86. Intramolecular electron transfer in simple model systems: A propagator study

    Article • The Journal of Chemical Physics, February 1977, American Institute of Physics

    Mary Ondrechen

  87. Intramolecular electron transfer: Simple theory of purely electronic effects

    Article • Molecular Physics, November 1976, Taylor & Francis

    Mary Ondrechen

  88. A treatment of vibrational relaxation without the rotating wave approximation

    Article • Chemical Physics, August 1976, Elsevier

    Mary Ondrechen