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M. Ondrechen · SciRah

Researcher profile · Semantic Scholar

M. Ondrechen

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M. Ondrechen — researcher profile on SciRah

h-index: 31
Works: 159
Citations: 3,188

Most-cited papers

Biochemical functional predictions for protein structures of unknown or uncertain function
Caitlyn L. Mills, P. Beuning, M. Ondrechen
2015Computational and Structural Biotechnology Journal91 citations Open access
Semantic Scholar
The need to implement FAIR principles in biomolecular simulations
R. Amaro, J. Åqvist, Ivet Bahar, F. Battistini +125 more
2024Nature Methods80 citations Open access
Semantic Scholar
Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties
W. Tong, Ying Wei, L. F. Murga, M. Ondrechen +1 more
2009PLoS Comput. Biol.75 citations Open access
Semantic Scholar
Identification of Functional Subclasses in the DJ-1 Superfamily Proteins
Wei Ying, D. Ringe, M. Wilson, M. Ondrechen
2007PLoS Comput. Biol.74 citations Open access
Semantic Scholar
Selective prediction of interaction sites in protein structures with THEMATICS
Ying Wei, J. Ko, L. F. Murga, M. Ondrechen
2007BMC Bioinformatics68 citations Open access
Semantic Scholar
Pharmacological Validation of Trypanosoma brucei Phosphodiesterases B1 and B2 as Druggable Targets for African Sleeping Sickness
N. Bland, Cuihua Wang, C. Tallman, A. Gustafson +13 more
2011Journal of Medicinal Chemistry50 citations Open access
Semantic Scholar
Evidence for Participation of Remote Residues in the Catalytic Activity of Co-type Nitrile Hydratase from Pseudomonas putida
H. Brodkin, W. R. Novak, A. Milne, J. D'Aquino +7 more
2011Biochemistry49 citations Open access
Semantic Scholar
High-performance prediction of functional residues in proteins with machine learning and computed input features.
Srinivas Somarowthu, Huyuan Yang, D. G. Hildebrand, M. Ondrechen
2011Biopolymers49 citations
Semantic Scholar
pH-dependent interdomain tethers of CD1b regulate its antigen capture.
M. Relloso, T. Cheng, Jin S. Im, E. Parisini +8 more
2008Immunity49 citations Open access
Semantic Scholar
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, Rishi Kapoor +3 more
2012European journal of medicinal chemistry47 citations Open access
Semantic Scholar
In vitro and In vivo evaluation of 11C-labeled azetidine-carboxylates for imaging monoacylglycerol lipase by PET imaging studies
Ran Cheng, Wakana Mori, Longle Ma, M. Alhouayek +22 more
2018Journal of Medicinal Chemistry44 citations Open access
Semantic Scholar
Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines
W. Tong, Ronald J. Williams, Ying Wei, L. F. Murga +2 more
2008Protein Science40 citations Open access
Semantic Scholar
A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase.
Srinivas Somarowthu, Heather R. Brodkin, J. D'Aquino, D. Ringe +2 more
2011Biochemistry37 citations
Semantic Scholar
Identification of residues in DmsD for twin-arginine leader peptide binding, defined through random and bioinformatics-directed mutagenesis.
Catherine S. Chan, T. Winstone, Limei Chang, C. M. Stevens +6 more
2008Biochemistry37 citations Open access
Semantic Scholar
Prediction of distal residue participation in enzyme catalysis
H. Brodkin, Nicholas A. DeLateur, Srinivas Somarowthu, Caitlyn L. Mills +4 more
2015Protein Science32 citations Open access
Semantic Scholar
“How Do We Do This at a Distance?!” A Descriptive Study of Remote Undergraduate Research Programs during COVID-19
Olivia A. Erickson, Rebecca Cole, Jared M. Isaacs, S. Álvarez-Clare +40 more
2021bioRxiv30 citations Open access
Semantic Scholar
Tri-arginine exosite patch of caspase-6 recruits substrates for hydrolysis
D. MacPherson, Caitlyn L. Mills, M. Ondrechen, J. Hardy
2018Journal of Biological Chemistry25 citations Open access
Semantic Scholar
Effects of non‐catalytic, distal amino acid residues on activity of E. coli DinB (DNA polymerase IV)
J. Walsh, Ramya Parasuram, Pradyumna R. Rajput, E. Rozners +2 more
2012Environmental and Molecular Mutagenesis24 citations Open access
Semantic Scholar
Prediction of Active Site and Distal Residues in E. coli DNA Polymerase III alpha Polymerase Activity.
Ramya Parasuram, Timothy A. Coulther, J. Hollander, Elise Keston-Smith +2 more
2018Biochemistry21 citations Open access
Semantic Scholar
Functional classification of protein 3D structures from predicted local interaction sites.
Ramya Parasuram, Joslynn S. Lee, Pengcheng Yin, Srinivas Somarowthu +1 more
2010Journal of Bioinformatics and Computational Biology21 citations
Semantic Scholar
Amino acid interactions that facilitate enzyme catalysis.
Timothy A. Coulther, J. Ko, M. Ondrechen
2021Journal of Chemical Physics20 citations Open access
Semantic Scholar
Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs)
Zhouxi Wang, Pengcheng Yin, Joslynn S. Lee, Ramya Parasuram +2 more
2013BMC Bioinformatics19 citations Open access
Semantic Scholar
A community effort in SARS-CoV-2 drug discovery
Johannes Schimunek, Philipp Seidl, Katarina Elez, Tim Hempel +148 more
2023Molecular Informatics15 citations Open access
Semantic Scholar
Virtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research Experiences
Riley A. Hess, Olivia A. Erickson, Rebecca Cole, Jared M. Isaacs +39 more
2022bioRxiv15 citations Open access
Semantic Scholar
Cartilage targeting cationic peptide carriers display deep cartilage penetration and retention in a rabbit model of post-traumatic osteoarthritis
Timothy L. Boyer, Olivia Chao, Bill Hakim, Luke Childress +5 more
2025Osteoarthritis and Cartilage14 citations Open access
Semantic Scholar
Enzyme active sites: Identification and prediction of function using computational chemistry.
Kelly K. Barnsley, M. Ondrechen
2022Current Opinion in Structural Biology13 citations Open access
Semantic Scholar
Fluorinated Adenosine A2A Receptor Antagonists Inspired by Preladenant as Potential Cancer Immunotherapeutics
Geng-Yang Yuan, Tanner C. Jankins, C. G. Patrick, Phaethon Philbrook +8 more
2017International Journal of Medicinal Chemistry13 citations Open access
Semantic Scholar
Design and evaluation of xanthine based adenosine receptor antagonists: Potential hypoxia targeted immunotherapies
R. Thomas, Joslynn S. Lee, V. Chevalier, Sara Sadler +5 more
2013Bioorganic & Medicinal Chemistry13 citations Open access
Semantic Scholar
Prediction of interaction sites from apo 3D structures when the holo conformation is different
L. F. Murga, M. Ondrechen, D. Ringe
2008Proteins: Structure, Function, and Bioinformatics13 citations
Semantic Scholar
Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity
G. Han, J. Ko, C. Farr, M. Deller +12 more
2011Proteins: Structure, Function, and Bioinformatics12 citations Open access
Semantic Scholar
Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS
Md Amin Hossain, Richa Sarin, Daniel P. Donnelly, Brandon C. Miller +34 more
2024PLoS Biology11 citations Open access
Semantic Scholar
Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase
L. Ngu, Jenifer N. Winters, Kien Nguyen, K. Ramos +5 more
2020PLoS ONE10 citations Open access
Semantic Scholar
Design, synthesis, and characterization of [18F]mG2P026 as a high contrast PET imaging ligand for metabotropic glutamate receptor 2
Geng-Yang Yuan, M. Dhaynaut, N. Guehl, S. Afshar +10 more
2021bioRxiv9 citations Open access
Semantic Scholar
Functional classification of protein structures by local structure matching in graph representation
Caitlyn L. Mills, Rohan Garg, Joslynn S. Lee, Liang Tian +4 more
2018Protein Science9 citations Open access
Semantic Scholar
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 +2 more
2016Methods9 citations Open access
Semantic Scholar
Functional Characterization of Structural Genomics Proteins in the Crotonase Superfamily.
Caitlyn L. Mills, Pengcheng Yin, Becky Leifer, Lori Ferrins +3 more
2022ACS Chemical Biology8 citations Open access
Semantic Scholar
Electrostatic fingerprints of catalytically active amino acids in enzymes
Suhasini M. Iyengar, Kelly K. Barnsley, Rholee Xu, A. Prystupa +1 more
2022Protein Science8 citations Open access
Semantic Scholar
Reintegrating Biology Through the Nexus of Energy, Information, and Matter.
K. Hoke, Sara L. Zimmer, A. Roddy, M. Ondrechen +2 more
2021Integrative and Comparative Biology8 citations Open access
Semantic Scholar
Design, Synthesis and Characterization of Benzimidazole Derivatives as PET Imaging Ligands for Metabotropic Glutamate Receptor 2 (mGluR2).
Geng-Yang Yuan, Xiying Qu, Baohui Zheng, Ramesh Neelamegam +10 more
2020Journal of Medicinal Chemistry7 citations Open access
Semantic Scholar
Computed protonation properties: unique capabilities for protein functional site prediction.
L. F. Murga, Wei Ying, M. Ondrechen
2007Genome informatics. International Conference on Genome Informatics6 citations
Semantic Scholar
Functional annotation of haloacid dehalogenase superfamily structural genomics proteins.
Lakindu S. Pathira Kankanamge, Lydia A Ruffner, Mong Mary Touch, M. Piña +2 more
2023Biochemical Journal5 citations Open access
Semantic Scholar
Biochemical Activity of 17 Cancer-Associated Variants of DNA Polymerase Kappa Predicted by Electrostatic Properties
Lakindu S. Pathira Kankanamge, A. Mora, M. Ondrechen, P. Beuning
2023Chemical Research in Toxicology4 citations Open access
Semantic Scholar
Best Practices to Diversify Chemistry Faculty
M. Agan, Reni Joseph, A. Rivera-Figueroa, Benny C. Chan +5 more
2021Journal of Chemical Education4 citations Open access
Semantic Scholar
Synthesis and Characterization of 5-(2-Fluoro-4-[11C]methoxyphenyl)-2,2-dimethyl-3,4-dihydro-2H-pyrano[2,3-b]pyridine-7-carboxamide as a PET Imaging Ligand for Metabotropic Glutamate Receptor 2
Geng-Yang Yuan, M. Dhaynaut, Yuheng Lan, N. Guehl +14 more
2022Journal of Medicinal Chemistry3 citations Open access
Semantic Scholar
Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase
Timothy A. Coulther, M. Pott, C. Zeymer, D. Hilvert +1 more
2021Protein Science3 citations Open access
Semantic Scholar
Synthesis of benzoylbenzamide derivatives of 17&agr;‐E‐vinyl estradiol and evaluation as ligands for the estrogen receptor‐&agr; ligand binding domain
R. Hanson, E. Mccaskill, Edward Hua, P. Tongcharoensirikul +6 more
2019Steroids3 citations Open access
Semantic Scholar
High Conservation of Amino Acids with Anomalous Protonation Behavior
D. G. Hildebrand, Huyuan Yang, M. Ondrechen, Ronald J. Williams
20103 citations
Semantic Scholar
Protein crosslinking as a therapeutic strategy for SOD1-related ALS
Md Amin Hossain, Richa Sarin, Daniel P. Donnelly, Brandon C. Miller +18 more
2021bioRxiv2 citations Open access
Semantic Scholar
A Practical Synthesis of Glycinamide Ribonucleotide
G. O'Doherty, P. Beuning, M. Ondrechen, Debarpita Ray
20182 citations Open access
Semantic Scholar
American Indian Science and Engineering Society (AISES): Building a Successful Model for Diversity and Inclusion
M. Ondrechen
20142 citations
Semantic Scholar

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P. Beuning×13
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P. Beuning — researcher profile on SciRah
Caitlyn L. Mills×6
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Caitlyn L. Mills — researcher profile on SciRah
L. F. Murga×6
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L. F. Murga — researcher profile on SciRah
D. Ringe×6
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Srinivas Somarowthu

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Suhasini M. Iyengar×6

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Geng-Yang Yuan×5

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Ramya Parasuram×5

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J. Ko — researcher profile on SciRah

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Zhouxi Wang — researcher profile on SciRah

Timothy A. Coulther×4

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Timothy A. Coulther — researcher profile on SciRah

Joslynn S. Lee×4

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Joslynn S. Lee — researcher profile on SciRah