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Quantum Chemical Prediction of Electron Ionization Mass Spectra of Trimethylsilylated Metabolites.
Anal Chem. 2022 Jan 25;94(3):1559-1566. doi: 10.1021/acs.analchem.1c02838. Epub 2022 Jan 10.
Anal Chem. 2022.
PMID: 35006668
How Well Can We Predict Mass Spectra from Structures? Benchmarking Competitive Fragmentation Modeling for Metabolite Identification on Untrained Tandem Mass Spectra.
Bremer PL, Vaniya A, Kind T, Wang S, Fiehn O.
Bremer PL, et al.
J Chem Inf Model. 2022 Sep 12;62(17):4049-4056. doi: 10.1021/acs.jcim.2c00936. Epub 2022 Aug 31.
J Chem Inf Model. 2022.
PMID: 36043939
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Beyond the Ground State: Predicting Electron Ionization Mass Spectra Using Excited-State Molecular Dynamics.
Wang S, Kind T, Bremer PL, Tantillo DJ, Fiehn O.
Wang S, et al. Among authors: bremer pl.
J Chem Inf Model. 2022 Sep 26;62(18):4403-4410. doi: 10.1021/acs.jcim.2c00597. Epub 2022 Sep 15.
J Chem Inf Model. 2022.
PMID: 36107950
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The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC-TOF MS metabolome samples.
Bremer PL, Wohlgemuth G, Fiehn O.
Bremer PL, et al.
J Cheminform. 2023 Jul 20;15(1):66. doi: 10.1186/s13321-023-00734-8.
J Cheminform. 2023.
PMID: 37475020
Free PMC article.
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SMetaS: A Sample Metadata Standardizer for Metabolomics.
Bremer PL, Fiehn O.
Bremer PL, et al.
Metabolites. 2023 Aug 12;13(8):941. doi: 10.3390/metabo13080941.
Metabolites. 2023.
PMID: 37623884
Free PMC article.
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Overcoming the Heuristic Nature of k-Means Clustering: Identification and Characterization of Binding Modes from Simulations of Molecular Recognition Complexes.
Bremer PL, De Boer D, Alvarado W, Martinez X, Sorin EJ.
Bremer PL, et al.
J Chem Inf Model. 2020 Jun 22;60(6):3081-3092. doi: 10.1021/acs.jcim.9b01137. Epub 2020 May 19.
J Chem Inf Model. 2020.
PMID: 32383869
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Understanding the enzyme-ligand complex: insights from all-atom simulations of butyrylcholinesterase inhibition.
Alvarado W, Bremer PL, Choy A, Dinh HN, Eung A, Gonzalez J, Ly P, Tran T, Nakayama K, Schwans JP, Sorin EJ.
Alvarado W, et al. Among authors: bremer pl.
J Biomol Struct Dyn. 2020 Mar;38(4):1028-1041. doi: 10.1080/07391102.2019.1596836. Epub 2019 Apr 7.
J Biomol Struct Dyn. 2020.
PMID: 30909811
Free PMC article.
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