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Gepasi is mainly a research tool. If you use it as part of your research you should cite Gepasi where appropriatly in
your publications. These are the papers that describe Gepasi:
Gepasi was used as a research tool in the following published research:
(81 papers)
2002
2001
- Bezemer, E. and Rutan, S. C. (2001).
"Multivariate curve resolution with non-linear fitting of kinetic profiles."
Chemometrics and Intelligent Laboratory Systems 59, 19-31.
- Bezemer, E. and Rutan, S. (2001).
"Study of the hydrolysis of a sulfonylurea herbicide using liquid chromatography with diode array detection and mass spectrometry by three-way multivariate curve resolution-alternating least squares."
Analytical Chemistry 73, 4403-4409.
- Brownback, M. A., Murmann, R. K., et al. (2001).
"Kinetic, thermodynamic and X-ray crystal studies on N-alkyl-alpha-amineoxime ligand exchange between planar nickel(II) complexes."
Polyhedron 20, 2505-2515.
- Eliasson, A., Hofmeyr, J. H. S., et al. (2001).
"The xylose reductase/xylitol dehydrogenase/xylulokinase ratio affects product formation in recombinant xylose-utilising Saccharomyces cerevisiae."
Enzyme and Microbial Technology 29, 288-297.
- Faller, P., Debus, R. J., et al. (2001).
"Rapid formation of the stable tyrosyl radical in photosystem II."
Proceedings of the National Academy of Sciences USA 98, 14368-14373.
- Hall, D. and Parsons, S. (2001).
"Non-surmountable antagonism: a general drawback of pre-steady- state measurement?"
Trends in Pharmacological Sciences 22, 63-65.
- Karpukhin, O. N. (2001).
"Reversible living polymerization and the Becker-Doring process."
Polymer Science Series A 43, 172-179.
- Klaning, U. K. and Sehested, K. (2001).
"Tellurium(V). A pulse radiolysis study."
Journal of Physical Chemistry A 105, 6637-6645.
- Kukkonen, J. P., Nasman, J., et al. (2001).
"Modelling of promiscuous receptor-G(i)/G(s) - protein coupling and effector response."
Trends in Pharmacological Sciences 22, 616-622.
- Leveau, J. H. J. and Lindow, S. E. (2001).
"Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria."
Journal of Bacteriology 183, 6752-6762.
- Martins, A. M., Mendes, P., et al. (2001).
"In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae."
European Journal of Biochemistry 268, 3930-3936.
- Mortensen, R. W., Corcoran, O., et al. (2001).
"S-naproxen-ss-1-O-acyl glucuronide degradation kinetic studies by stopped-flow high-performance liquid chromatography-H-1 NMR and high-performance liquid chromatography-UV."
Drug Metabolism and Disposition 29, 375-380.
- Plesner, I. W., Bulow, A., et al. (2001).
"Accurate determination of rate constants of very slow, tight-binding competitive inhibitors by numerical solution of differential equations, independently of precise knowledge of the enzyme concentration."
Analytical Biochemistry 295, 186-193.
- Reijenga, K. A., Snoep, J. L., et al. (2001).
"Control of glycolytic dynamics by hexose transport in Saccharomyces cerevisiae."
Biophysical Journal 80, 626-634.
- Rivas, F. J., Beltran, F. J., et al. (2001).
"Treatment of olive oil mill wastewater by Fenton's reagent."
Journal of Agricultural and Food Chemistry 49, 1873-1880.
- Strasser, R. J. and Stirbet, A. D. (2001).
"Estimation of the energetic connectivity of PSII centres in plants using the fluorescence rise O-J-I-P - Fitting of experimental data to three different PSII models."
Mathematics and Computers in Simulation 56, 451-461.
- Sukal, S. and Leyh, T. S. (2001).
"Product release during the first turnover of the ATP sulfurylase-GTPase."
Biochemistry 40, 15009-15016.
- Venning, J. D., Rodrigues, D. J., et al. (2001).
"The heterotrimer of the membrane-peripheral components of transhydrogenase and the alternating-site mechanism of proton translocation."
Journal of Biological Chemistry 276, 30678-30685.
2000
- Ashton, P.R., Calcagno, P. et al (2000).
"Using Polarization Effects to Alter Chemical Reactivity: A Simple Host Which Enhances Amine Nucleophilicity"
Organic Letters 2, 1365-1368.
- Brightman, F.A. and Fell, D.A. (2000).
"Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells."
FEBS Letters 482, 169-174. Supplementary material here
- Brown, M.J.B., Mensah, L.M. et al (2000).
"Rational design of femtomolar inhibitors of isoleucyl tRNA synthetase from a binding model for pseudomonic acid-A"
Biochemistry 39, 6003-6011.
- Chang, J. Y., Li, L. et al. (2000).
"The underlying mechanism for the diversity of disulfide folding pathways."
Journal of Biological Chemistry 275 8287-8289.
- Fedosov, S.N., Fedosova, N.U. et al. (2000).
"Conformational changes of transcobalamin induced by aquocobalamin binding - Mechanism of substitution of the cobalt-coordinated group in the bound ligand."
Journal of Biological Chemistry 275 11791-11798.
- Hall, J.G., Eis, P.S. et al. (2000).
"Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction."
Proceedings of the National Academy of Sciences USA 97, 8272-8277.
- Hennig, L., Buche, C. and Schäfer, E. (2000).
"Degradation of phytochrome A and the high irradiance response in Arabidopsis: a kinetic analysis."
Plant Cell and Environment 23, 727-734.
- Hofmeyr, J. H. S. and Cornish-Bowden, A. (2000).
"Regulating the cellular economy of supply and demand."
FEBS Letters 476, 47-51.
- Johnsen, L.B., Rasmunssen, L.K. et al. (2000).
"Kinetic and structural characterization of a two-domain streptokinase: dissection of domain functionality"
Biochemistry 39, 6440-6448.
- Karpukhin, O.N. (2000).
"Anomalous large times of creation of ensembles of particles interacting by Becker-Döring equation."
Doklady Akademii Nauk 371, 25-27.
- Martinez-Force, E. and Garces, R. (2000).
"Metabolic control analysis of de novo sunflower fatty acid biosynthesis."
Biochemical Society Transactions 28, 669-671.
- Petrascu, A.-M. (2000)
"A contribution to the study of oscillating chemical and biochemical reactions"
Ph.D. thesis, Catholic University of Leuven, Belgium.
- Rais, B., Ortega, F. et al. (2000).
"Quantitative characterization of homo- and heteroassociations of muscle phosphofructokinase with aldolase"
Biochimica et Biophysica Acta 1479, 303-314.
- Rowe, H.L., Spencer, N. and Philp, D. (2000).
"Acceleration of a dipolar cycloaddition by a simple bisamide receptor."
Tetrahedron Letters 41, 4475-4479.
- Rushing, C. W., Thompson, R. C., et al. (2000).
"General model for the nonlinear pH dynamics in the oxidation of sulfur(-II) species."
Journal of Physical Chemistry A 104, 11561-11565.
- Thornalley, P. J., Yurek-George, A., et al. (2000).
"Kinetics and mechanism of the reaction of aminoguanidine with the alpha-oxoaldehydes glyoxal, methylglyoxal, and 3-deoxyglucosone under physiological conditions."
Biochemical Pharmacology 60, 55-65.
1999
- Alvarez, B., Ferrer-Sueta, G. et al (1999).
"Kinetics of peroxynitrite reaction with amino acids and human serum albumin."
Journal of Biological Chemistry 274, 842-848.
- Bennes, R., Philp, D. et al (1999).
"Recognition-Mediated Facilitation of a Disfavored Diels-Alder Reaction"
Organic Letters 1, 1087-1090.
- Bonini, M.G., Radi, R.et al (1999).
"Direct EPR detection of the carbonate radical anion produced from peroxynitrite and carbon dioxide."
Journal of Biological Chemistry 274, 10802-10806.
- Culot, L. (1999).
"Predicted occupancy of class-1 cytokine receptors in systems involving two bivalent ligands"
PhD thesis, Harvard University.
- Ferrer-Sueta, G., Batinic-Haberle, I. et al. (1999).
"Catalytic scavenging of peroxynitrite by isomeric Mn(III) N- methylpyridylporphyrins in the presence of reductants."
Chemical Research in Toxicology 12, 442-449.
- Gerendasy, D. (1999).
"Homeostatic tuning of Ca2+ signal transduction by members of the calpacitin protein family."
Journal of Neuroscience Research 58, 107-119.
- Grotjohann, I., Schulzke, J.D. and Fromm, M. (1999).
"Electrogenic Na+ transport in rat late distal colon by natural and synthetic glucocorticosteroids."
American Journal of Physiology 39, G491-G498.
- Hein, H., Hoffmann, A. and Zellner, R. (1999).
"Direct investigations of reactions of 1-butoxy and 1-pentoxy radicals using laser pulse initiated oxidation: reaction with O-2 and isomerisation at 293 K and 50 mbar."
Physical Chemistry Chemical Physics 1, 3743-3752.
- Krooshof, G. H., Floris, R. et al. (1999).
"Thermodynamic analysis of halide binding to haloalkane dehalogenase suggests the occurrence of large conformational changes."
Protein Science 8, 355-360.
- McCaskill, D. and Croteau, R. (1999).
"Isopentenyl diphosphate is the terminal product of the deoxyxylulose-5-phosphate pathway for terpenoid biosynthesis in plants."
Tetrahedron Letters 40, 653-656.
- Mosinger, B.J. (1999).
"Higher cholesterol in human LDL is associated With the increase of oxidation susceptibility and the decrease of antioxidant defence: experimental and simulation data."
Biochimica et Biophysica Acta 1453, 180-184.
- Petrasco, A.-M., Koch, M.H.J. and Försterling, H.-D. (1999).
"Effect of Oxygen on the Belousov-Zhabotinsky Reaction at Low Cerium Concentrations "
Journal of Physical Chemistry A 103, 6757-6765.
- Umschlag, T. and Herrmann, H. (1999).
"The carbonate radical (HCO3dot/CO3-dot) as a reactive intermediate in water chemistry: Kinetics and modelling."
Acta Hydrochimica et Hydrobiologica 27, 214-222.
- van Thor, J.J., Geerlings, T.H. et al. (1999).
"Kinetic evidence for the PsaE-dependent transient ternary complex photosystem I/ferredoxin/ferredoxin : NADP(+) reductase in a cyanobacterium."
Biochemistry 38, 12735-12746.
1998
- Birkenmeier, G., I. Kampfer, et al. (1998). "Human leptin forms completes with alpha 2-macroglobulin which are recognized by the alpha 2-macroglobulin receptor/low density lipoprotein receptor-related protein." European Journal of Endocrinology 139, 224-230.
- Eisenthal, R., A. Cornish-Bowden (1998). "Prospects for antiparasitic drugs. The case of Trypanosoma brucei, the causative agent of African sleeping sickness." Journal of Biological Chemistry 273, 5500-5505.
- Hein, H., Hoffmann, A.and Zellner, R. (1998). "Direct investigations of reactions of 2-butoxy radicals using laser pulse initiated oxidation: Reaction with O-2 and unimolecular decomposition at 293 K and 50 mbar" Berichte der Bunsengesellschaft Physical Chemistry 102, 1840-1849.
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Johnsen LB, Ravn P et al. (1998). "A refined kinetic analysis of plasminogen activation by recombinant bovine tissue-type plasminogen activator indicates two interconvertible activator forms." Biochemistry 37, 12631-12639.
- Kukkonen, J. P., Nasman, J. et al. (1998). "Pseudo-noncompetitive antagonism of M-1, M-3, and M-5, muscarinic receptor-mediated Ca2- mobilization by muscarinic antagonists." Biochemical and Biophysical Research Communications 243, 41-46.
- Ng, K.K.S. and Weis, W.I. (1998) "Coupling of prolyl peptide bond isomerization and Ca2+ binding in a C-type mannose-binding protein." Biochemistry 37, 17977-17989.
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Pope, AJ, Lapointe, J et al. (1998a). "
Characterization of isoleucyl-tRNA synthetase from Staphylococcus aureus. I: kinetic mechanism of the substrate activation reaction studied by transient and steady-state techniques." Journal of Biological Chemistry 273, 31680-31690.
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Pope, AJ, Lapointe, J et al. (1998b). "
Characterization of isoleucyl-tRNA synthetase from Staphylococcus aureus. II: mechanism of inhibition by reaction intermediate and pseudomonic acid analogues studied using transient and steady-state kinetics. " Journal of Biological Chemistry 273, 31691-31701.
1997
- Abuja, P. M., R. Albertini et al.(1997). "Simulation of the induction of oxidation of low-density lipoprotein by high copper concentrations: evidence for a nonconstant rate of initiation."
Chem. Res. Toxicol. 10(6), 644 - 651.
- Krooshof, G. H., E. M. Kwant, et al. (1997). "Repositioning the catalytic triad aspartic acid of haloalkane dehalogenase: Effects on stability, kinetics, and structure." Biochemistry 36(31), 9571-9580.
- Mendes, P. (1997). " Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. " Trends Biochem. Sci. 22, 361-363.
- Padmaja, S., G. L. Squadrito, et al. (1997). "Peroxynitrite-mediated oxidation of D,L-selenomethionine: Kinetics, mechanism and the role of carbon dioxide." Free Radical Biology and Medicine 23, 917-926.
- Pryor, W. A., J. N. Lemercier, et al. (1997). "The catalytic role of carbon dioxide in the decomposition of peroxynitrite." Free Radical Biology and Medicine 23, 331-338.
- Schanstra, J. P., A. Ridder, et al. (1997). "Influence of mutations of val226 on the catalytic rate of haloalkane dehalogenase." Protein Engineering 10, 53-61.
- Zhang, H. W., G. L. Squadrito, et al. (1997). "Inhibition of peroxynitrite-mediated oxidation of glutathione by carbon dioxide." Archives of Biochemistry and Biophysics 339, 183-189.
- Zhang, H. W., G. L. Squadrito, et al. (1997). "The mechanism of the peroxynitrite carbon dioxide reaction probed using tyrosine." Nitric Oxide Biology and Chemistry 1, 301-307.
1996
- Glaser, R.W. and Hausdorf, G. (1996)"Binding kinetics of an antibody against hiv p24 core protein measured with real-time biomolecular interaction analysis suggest a slow conformational change in antigen p24" Journal of Immunological Methods 189, 1-14.
- Mendes, P. and D. B. Kell (1996). "On the analysis of the inverse problem of metabolic pathways using artificial neural networks." BioSystems 38(1): 15-28.
- Mendes, P., D. B. Kell, et al. (1996). "Why and when channeling can decrease pool size at constant net flux in a simple dynamic channel." Biochimica et Biophysica Acta 1289(2): 175-186.
- Schanstra, J. P., J. Kingma, et al. (1996). "Specificity and kinetics of haloalkane dehalogenase." Journal of Biological Chemistry 271(25): 14747-14753.
- Schanstra, J. P., I. S. Ridder, et al. (1996). "Kinetic characterization and X-ray structure of a mutant of haloalkane dehalogenase with higher catalytic activity and modified substrate range." Biochemistry 35(40): 13186-13195.
- Stirbet, A. D. and R. J. Strasser (1996). "Numerical simulation of the in vivo fluorescence in plants." Mathematics and Computers in Simulation 42(2-3): 245-253.
- Torres, N. V. (1996). "Metabolic control analysis of inhibitory feedback interaction. Application to biotechnological processes." Journal of Theoretical Biology 182, 405-410.
1995
- Abuja, P. M. and H. Esterbauer (1995). "Simulation of lipid peroxidation in low-density-lipoprotein by a basic skeleton of reactions." Chemical Research in Toxicology 8(5): 753-763.
- Giersch, C. (1995). "Concerning the measurement of flux control coefficients by enzyme titration. Steady states, quasi-steady states, and the role of time in control analytical experiments." European Journal of Biochemistry 231(3): 587-592.
- Mendes, P., D. B. Kell, et al. (1995). "A series of cases in which metabolic channeling can decrease the pool size at constant net flux in a simple dynamic channel." Biochemical Society Transactions 23(2): S 287-s 287.
- Stirbet, A. D. and R. J. Strasser (1995). "Numerical simulation of the fluorescence induction in plants." Archives des Sciences 48(1): 41-59.
- Stirbet, A. D., Govindjee, et al. (1995). "Numerical simulation of clorophyll A fluorescence induction in plants." in Photosynthesis: from light to biosphere. P. Mathis (ed.), Vol II pp. 919-922.
before 1995
- Mendes, P. and D. B. Kell (1994). Control analysis of metabolic channeling. Modern Trends in Biothermokinetics. S. Schuster, M. Rigoulet, R. Ouhabi and J.-P. Mazat eds. New York & London, Plenum Press: 211-216.
- Mendes, P. (1994).
"Computer simulation of the dynamics of biochemical pathways.". (Ph.D. thesis) Department of Biological Sciences. Aberystwyth, University of Wales.
- Mendes, P. and D. B. Kell (1993). "On the role of enzyme kinetic parameters in determining the effectiveness with which channelling can decrease the size of a metabolite pool." Acta Biotheoret. 41: 63-73.
- Mendes, P., D. B. Kell, et al. (1992). "Channelling can decrease pool size." Eur. J. Biochem. 204: 257-266.
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