COPASI's Use In Biochemistry

Chushak Y, Harbaugh S, Zimlich K, Alfred B, Chávez J, Kelley-Loughnane N (2021) Characterization of synthetic riboswitch in cell-free protein expression systems. RNA Biology doi:10.1080/15476286.2020.1868149 Biochemistry Genetics Link
Novichkov AI, Hanopolskyi AI, Miao X, Shimon LJW, Diskin-Posner Y, Semenov SN (2021) Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization. Nature Communications 12:2994 Biochemistry Link
Ritis D (2021) Dynamical modeling in biological networks. Masters Thesis, Democritus University of Thrace, Greece. Biochemistry Link

3 publications
Barrett TM (2020) Thioamides and proteolysis: Examining the effects and applications of a single-atom substitution. PhD Thesis, University of Pennsylvania. Biochemistry Link
Benchoam D, Semelak JA, Cuevasanta E, Mastrogiovanni M, Grassano JS, Ferrer-Sueta G, Zeida A, Trujillo M, Möller MN, Estrin DA, Alvarez B (2020) Acidity and nucleophilic reactivity of glutathione persulfide. Journal of Biological Chemistry 295:15466–15481 Biochemistry Link
Benedek Z, Papp M, Oláh J, Szilvási T (2020) Demonstrating the Direct Relationship between Hydrogen Evolution Reaction and Catalyst Deactivation in Synthetic Fe Nitrogenases. ACS Catalysis 10:12555–12568 Biochemistry Link
Bragança CE, Kraut DA (2020) Mode of targeting to the proteasome determines GFP fate. Journal of Biological Chemistry 295:15892–15901 Biochemistry Link
Fournié M, Truan G (2020) Multiplicity of carotene patterns derives from competition between phytoene desaturase diversification and biological environments. Scientific Reports 10:21106 Biochemistry Metabolism Link
Padayachee L, Rohwer JM, Pillay CS (2020) The thioredoxin redox potential and redox charge are surrogate measures for flux in the thioredoxin system. Archives of Biochemistry and Biophysics 680:108231 Biochemistry Metabolism Link
Schmallegger M, Barbon A, Bortolus M, Chemelli A, Bilkis I, Gescheidt G, Weiner L (2020) Systematic Quantification of Electron Transfer in a Bare Phospholipid Membrane Using Nitroxide-Labeled Stearic Acids: Distance Dependence, Kinetics, and Activation Parameters. Langmuir 36:10429–10437 Biophysics Biochemistry Link
Vasil’ev RF, Kancheva VD, Naumov VV, Slavova-Kazakova AK, Trofimov AV, Fedorova GF, Yablonskaya OI (2020) Extreme Kinetics of Chemiluminescence in the Initiated Oxidation of Vegetable Lipids. Russian Journal of Physical Chemistry B 14:479–482 Biochemistry Link
Zhu H, Poojary MM, Andersen ML, Lund MN (2020) The effect of molecular structure of polyphenols on the kinetics of the trapping reactions with methylglyoxal. Food Chemistry 319:126500 Biochemistry Link

9 publications
Adelson CN, Johnston EM, Hilmer KM, Watts H, Dey SG, Brown DE, Broderick JB, Shepard EM, Dooley DM, Solomon EI (2019) Characterization of the Preprocessed Copper Site Equilibrium in Amine Oxidase and Assignment of the Reactive Copper Site in Topaquinone Biogenesis. Journal of the American Chemical Society 141:8877–8890 Enzymology Biochemistry Link
Faraj SE, Noguera ME, Delfino JM, Santos J (2019) Global Implications of Local Unfolding Phenomena, Probed by Cysteine Reactivity in Human Frataxin. Scientific Reports 9:1–12 Biochemistry Link
Hochberg D, Ribó JM (2019) Entropic Analysis of Mirror Symmetry Breaking in Chiral Hypercycles. Life 9:28 Biochemistry Link
Macikova L, Sinica V, Kadkova A, Villette S, Ciaccafava A, Faherty J, Lecomte S, Alves ID, Vlachova V (2019) Putative interaction site for membrane phospholipids controls activation of TRPA1 channel at physiological membrane potentials. FEBS Journal 286:3664–3683 Signaling Biochemistry Link
Möller MN, Denicola A (2019) Acceleration of the autoxidation of nitric oxide by proteins. Nitric Oxide: Biology and Chemistry 85:28–34 Biochemistry Link
Muth M, Jänsch N, Kopranovic A, Krämer A, Wössner N, Jung M, Kirschhöfer F, Brenner-Weiß G, Meyer-Almes F-J (2019) Covalent inhibition of histone deacetylase 8 by 3,4-dihydro-2H-pyrimido[1,2-c][1,3]benzothiazin-6-imine. Biochimica et Biophysica Acta (BBA) - General Subjects 1863:577–585 Enzymology Biochemistry Link
Pawłowski PH, Szczęsny P, Rempoła B, Poznańska A, Poznański J (2019) Combined in silico and 19F NMR analysis of 5-fluorouracil metabolism in yeast at low ATP conditions. Bioscience Reports 39 9:BSR20192847 Biochemistry Link
Reader P (2019) in vitro Characterisation of the Complement Cascade for Predicting Patient Outcome Post-operatively. Ph.D. Thesis, University of Exeter Biochemistry Physiology Link
Sheppard S, Dikicioglu D (2019) Dynamic modelling of the killing mechanism of action by virus-infected yeasts. Journal of the Royal Society Interface 16:20190064 Biochemistry Signaling Link
Taheri M, Nouri K, Asgari Y, Zabihinpour Z, Sadeghi M (2019) The Significance of Noise in the Evolution of Negative and Positive Cooperativity in Protein Complexes. MATCH Communications in Mathematical and Computer Chemistry 81:177–192 Biochemistry Macromolecular Biochemistry Link
Virtanen O, Valev D, Kruse O, Wobbe L, TYYSTJÄRVI E (2019) Photoinhibition and continuous growth of the wild-type and a high-light tolerant strain of Chlamydomonas reinhardtii. Photosynthetica 57:617–626 Biochemistry Microbiology Link
Yu T (2019) Oxidative Protein Folding: Investigating New Enzymes, New Assays, and New Locations. PhD Thesis, University of Delaware. Biochemistry Link

12 publications
Carpine R, Raganati F, Olivieri G, Hellingwerf KJ, Pollio A, Salatino P, Marzocchella A (2018) Poly-β-hydroxybutyrate (PHB) production by Synechocystis PCC6803 from CO2: Model development. Algal Research 29:49–60 Microbiology Biochemistry Link
Coulthard SA, McGarrity S, Sahota K, Berry P, Redfern CP (2018) Three Faces of Mercaptopurine Cytotoxicity in vitro: Methylation, Nucleotide Homeostasis and Deoxythioguanosine in DNA. Drug Metabolism and Disposition 46:1191–1199 Toxicology Biochemistry Link
da Silva, LHG (2018) Self-Replication and Non-enzymatic Catalytic Networks subject to Open Flow. MS Thesis, University of Porto. Biochemistry Theory Link
da Silva LHG, Hochberg D (2018) Open flow non-enzymatic template catalysis and replication. Physical Chemistry Chemical Physics 20:14864–14875 Biochemistry Link
Fiebig D, Storka J, Roeder M, Meyners C, Schmelz S, Blankenfeldt W, Scrima A, Kolmar H, Fuchsbauer H-L (2018) Destructive twisting of neutral metalloproteases: the catalysis mechanism of the Dispase autolysis-inducing protein from Streptomyces mobaraensis DSM 40487. FEBS Journal 285:4246–4264 Biochemistry Link
Haffez H, Chisholm DR, Tatum NJ, Valentine R, Redfern C, Pohl E, Whiting A, Przyborski S (2018) Probing biological activity through structural modelling of ligand-receptor interactions of 2,4-disubstituted thiazole retinoids. Bioorganic & Medicinal Chemistry 26:1560–1572 Biochemistry Link
Kaushik AC, Kumar A, Dwivedi VD, Bharadwaj S, Kumar S, Bharti K, Kumar P, Chaudhary RK, Mishra SK (2018) Deciphering the Biochemical Pathway and Pharmacokinetic Study of Amyloid βeta-42 with Superparamagnetic Iron Oxide Nanoparticles (SPIONs) Using Systems Biology Approach. Molecular Neurobiology 55:3224–3236 Biochemistry Pharmacology Laboratory Method Link
Rossi F., Torbensen K., Ristori S., Abou-Hassan A. (2018) Signal Transduction and Communication Through Model Membranes in Networks of Coupled Chemical Oscillators. In: Pelillo M., Poli I., Roli A., Serra R., Slanzi D., Villani M. (eds.) Artificial Life and Evolutionary Computation. WIVACE 2017. Communications in Computer and Information Science, vol 830. Springer Biochemistry Signaling Link
Semenov SN, Ainla A, Skorb EV, Postma SG (2018) Four-Variable Model of an Enzymatic Oscillator Based on Trypsin. Israel Journal of Chemistry 58:781–786 Biochemistry Link
Wang M, Wölfer C, Otrin L, Ivanov I, Vidaković-Koch T, Sundmacher K (2018) Transmembrane NADH Oxidation with Tetracyanoquinodimethane. Langmuir 34:5435–5443 Biochemistry Biotechnology Link
Ximing L (2018) Insights into Delivery of Somatic Calcium Signals to the Nucleus During LTP Revealed by Computational Modeling. PhD Thesis, Ohio University Signaling Biochemistry Link
Xu H, Curtis TY, Powers SJ, Raffan S, Gao R, Huang J, Heiner M, Gilbert DR, Halford NG (2018) Genomic, biochemical and modelling analyses of asparagine synthetases from wheat. Frontiers in Plant Science 8:2237 Biochemistry Link
Yeom K-H, Mitchell S, Linares AJ, Zheng S, Lin C-H, Wang X-J, Hoffmann A, Black DL (2018) Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proceedings of the National Academy of Sciences USA 115:E11061–E11070 Genetics Biochemistry Link

13 publications
Amdahl MB, Sparacino-Watkins CE, Corti P, Gladwin MT, Tejero J (2017) Efficient Reduction of Vertebrate Cytoglobins by the Cytochrome b 5/Cytochrome b 5 Reductase/NADH System. Biochemistry 56:3993–4004 Biochemistry Enzymology Link
Haffez H, Chisholm DR, Valentine R, Pohl E, Redfern C, Whiting A (2017) The molecular basis of the interactions between synthetic retinoic acid analogues and the retinoic acid receptors. MedChemComm 8:578 Biochemistry Pharmacology Link
Orlenko A, Chi PB, Liberles DA (2017) Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways. BMC Evolutionary Biology 17:117 Biochemistry Genetics Link
Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT (2017) A proteomic approach to analyse the aspirin-mediated lysine acetylome. Molecular & Cellular Proteomics 16:310–326 Pharmacology Biochemistry Laboratory Method Link
Tikidji-Hamburyan A, Reinhard K, Storchi R, Dietter J, Seitter H, Davis KE, Idrees S, Mutter M, Walmsley L, Bedford RA, Ueffing M, Ala-Laurila P, Brown TM, Lucas RJ, Münch TA (2017) Rods progressively escape saturation to drive visual responses in daylight conditions. Nature Communications 8:1813 Biochemistry Biophysics Physiology Link
Wang H, Ray JCJ (2017) Dynamical predictors of an imminent phenotypic switch in bacteria. Physical Biology 14:045007 Microbiology Biochemistry Link
Zaccarin M, Bosello-Travain V, Di Paolo ML, Falda M, Maiorino M, Miotto G, Piccolo S, Roveri A, Ursini F, Venerando R, Toppo S (2017) Redox status in a model of cancer stem cells. Archives of Biochemistry and Biophysics 617:120–128 Biochemistry Cell Biology Link

7 publications
Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T (2016) Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science Advances 2:e1600823 Biochemistry Signaling Link
Haffez HRS (2016) Design, synthesis and biological evaluation of small molecules for controlling cellular development. PhD Thesis, Durham University, UK. Biochemistry Pharmacology Link
Ledwitch KV, Barnes RW, Roberts AG (2016) Unravelling the complex drug–drug interactions of the cardiovascular drugs, verapamil and digoxin, with P-glycoprotein. Bioscience Reports 36:e00309 Pharmacology Biochemistry Link
Ledwitch KV, Gibbs ME, Barnes RW, Roberts AG (2016) Cooperativity between verapamil and ATP bound to the efflux transporter P-glycoprotein. Biochemical Pharmacology 118:96–108 Pharmacology Biochemistry Link
McClary WD (2016) Interactions of Cytochrome P450 3A4 with Phospholipid Bilayer Nanodiscs. PhD Thesis, Seattle, University of Washington. Biochemistry Macromolecular Biochemistry Link
Olajuyigbe FM, Demitri N, De Zorzi R, Geremia S (2016) Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals. Molecules 21:1458 Biochemistry Link
Reichard EL, Chirico GG, Dewey WJ, Nassif ND, Bard KE, Millas NE, Kraut DA (2016) Substrate Ubiquitination Controls the Unfolding Ability of the Proteasome. Journal of Biological Chemistry 291:18547–18561 Biochemistry Macromolecular Biochemistry Link
Rentergent J, Driscoll MD, Hay S (2016) Time course analysis of enzyme-catalyzed DNA polymerization. Biochemistry 55:5622–5634 Biochemistry Enzymology Macromolecular Biochemistry Link
Semenov SN, Kraft LJ, Ainla A, Zhao M, Baghbanzadeh M, Campbell VE, Kang K, Fox JM, Whitesides GM (2016) Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions. Nature 537:656–660 Chemistry Biochemistry Link
Vranish JN, Das D, Barondeau DP (2016) Real-Time Kinetic Probes Support Monothiol Glutaredoxins As Intermediate Carriers in Fe–S Cluster Biosynthetic Pathways. ACS Chemical Biology 11:3114–3121 Enzymology Biochemistry Link

10 publications

0 publication
Sapra A, Ramadan D, Thorpe C (2014) Multivalency in the inhibition of oxidative protein folding by arsenic (III) species. Biochemistry 54:612–621 Biochemistry Link

1 publication
Emiola A, Falcarin P, Tocher J, George J (2013) A model for the proteolytic regulation of LpxC in the lipopolysaccharide pathway of Escherichia coli. Computational Biology and Chemistry 47:1–7 Biochemistry Microbiology Link

1 publication
Hamberg A, Maurer S, Hult K (2012) Rational engineering of Candida antarctica lipase B for selective monoacylation of diols. Chemical Communications 48:10013 Biochemistry Link
Kraut DA, Israeli E, Schrader EK, Patil A, Nakai K, Nanavati D, Inobe T, Matouschek A (2012) Sequence- and Species-Dependence of Proteasomal Processivity. ACS Chemical Biology 7:1444–1453 Biochemistry Macromolecular Biochemistry Link
Witmer JR (2012) Quantitative analysis and modeling of redox networks in biology. PhD Thesis, University of Iowa. Biochemistry Link

3 publications

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Friedrich A, Ghosh R, Kolb R, Herdtweck E, Schneider S (2009) Iridium Olefin Complexes Bearing Dialkylamino/amido PNP Pincer Ligands: Synthesis, Reactivity, and Solution Dynamics. Organometallics 28:708-718 Biochemistry Link
Katzberg, M., Wechler, K., Müller, M., Dünkelmann, P., Stohrer, J., Hummel, W., & Bertau, M. (2009). Biocatalytical production of (5S)-hydroxy-2-hexanone. Organic and Biomolecular Chemistry 7:304-314 Biochemistry Link
Kona F, Tao P, Martin P, Xu X, Gatti DL (2009) Electronic Structure of the Metal Center in the Cd 2+ , Zn 2+ , and Cu 2+ Substituted Forms of KDO8P Synthase: Implications for Catalysis. Biochemistry 48:3610–3630 Enzymology Biochemistry Link

3 publications

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