Ming Chen wrote:
> What else tools can be used to model and simulate biochemical reaction
> network except E-Cell, Gepsi...? Some DOS version tools seem to be out
> of date already.
The program DynaFit [P. Kuzmic (1996) Anal. Biochem. 237,
260-273] is useful in the analysis of complex reaction
mechanism, for which traditional (algebraic) kinetic
equations cannot be derived. In my opinion, the program's
utility in the simulation of biochemical reaction networks
has not been fully explored by workers in that area.
Attached below is a bibliography containing 54 journal
articles that cited DynaFit over the last three years. Most
citations are from articles in the journal Biochemistry,
followed by the Journal of Biological Chemistry, and
Biochimica & Biophysica Acta.
The main application of DynaFit seems to be in figuring out
biochemical reaction mechanisms from kinetic and/or
equilibrium data. However, the program has been used in
many different areas, such as environmental chemistry, food
chemistry, guest-host interactions, and structure-activity
studies.
The program is available free of charge to academic
researchers:
Home page: http://www.biokin.com/dynafit/
Download: http://www.biokin.com/dynafit/download.html
User manual: http://www.biokin.com/dynafit/scripting/
Please contact me if you have any questions about installing
or running the program.
Best Regards,
- P.K.
-------------------------------------------------------
P e t r K u z m i c, Ph. D. * BioKin Ltd.
1652 S. Grand Ave. * Suite 337 * Pullman, WA 99163
509.334.4131 * 509.332.3493 fax * http://www.biokin.com
COUNT JOURNAL
----- --------------------------------
12 Biochemistry
6 J. Biol. Chem.
3 Biochim. Biophys. Acta-Protein Struct. Molec. Enzym.
2 J. Am. Chem. Soc.
2 Biophys. J.
2 Proteins
2 Proc. Natl. Acad. Sci. U. S. A.
2 Anal. Biochem.
2 J. Org. Chem.
2 Biochem. J.
1 J. Chem. Educ.
1 Biochem. Biophys. Res. Commun.
1 FEBS Lett.
1 Chem. Res. Toxicol.
1 J. Mol. Biol.
1 Methods
1 J. Biomol. Struct. Dyn.
1 Anal. Chem.
1 Plant Cell Environ.
1 Protein Sci.
1 Bioinformatics
1 Nature
1 Food Res. Int.
1 J. Environ. Monit.
1 Clin. Chim. Acta
1 J. Sci. Food Agric.
1 Org. Lett.
1 Nucleic Acids Res.
1 Chem. Biol.
---------------------------------------
REFERENCES
1.
"Chain length-dependent affinity of helical foldamers for a
rodlike guest"
Tanatani, A; Mio, MJ; Moore, JS (2001)
J. Am. Chem. Soc. 123(8), 1792-1793.
2.
"Thermostable and site-specific DNA binding of the gene
product ORF56 from the Sulfolobus islandicus plasmid pRN1, a
putative archael plasmid copy control protein"
Lipps, G; Stegert, M; Krauss, G (2001)
Nucleic Acids Res. 29(4), 904-913.
3.
"Kinetic studies of Fos center dot Jun center dot DNA
complex formation: DNA binding prior to dimerization"
Kohler, JJ; Schepartz, A (2001)
Biochemistry 40(1), 130-142.
4.
"The N-terminal region of cystatin A (stefin A) binds to
papain subsequent to the two hairpin loops of the inhibitor.
Demonstration of two-step binding by rapid-kinetic studies
of cystatin A labeled at the N-terminus with a fluorescent
reporter group"
Estrada, S; Olson, ST; Raub-Segall, E; Bjork, I (2000)
Protein Sci. 9(11), 2218-2224.
5.
"Degradation of chlortoluron in water disinfection
processes: a kinetic study"
Losito, H; Zambonin, CG; Palmisano, F (2000)
J. Environ. Monit. 2(6), 582-586.
6.
"Functional roles of the conserved threonine 250 in the
target recognition domain of HhaI DNA methyltransferase"
Vilkaitis, G; Dong, AP; Weinhold, E; Cheng, XD;
Klimasauskas, S (2000)
J. Biol. Chem. 275(49), 38722-38730.
7.
"Characterization of enzymatic processes by rapid mix-quench
mass spectrometry: The case of dTDP-glucose 4,6-dehydratase"
Gross, JW; Hegeman, AD; Vestling, MM; Frey, PA (2000)
Biochemistry 39(45), 13633-13640.
8.
"X-ray structures of five renin inhibitors bound to
saccharopepsin: Exploration of active-site specificity"
Cronin, NB; Badasso, MO; Tickle, IJ; Dreyer, T; Hoover, DJ;
Rosati, RL; Humblet, CC; Lunney, EA; Cooper, JB (2000)
J. Mol. Biol. 303(5), 745-760.
9.
"The zinc metalloregulatory protein Synechococcus PCC7942
SmtB binds a single zinc ion per monomer with high affinity
in a tetrahedral coordination geometry"
VanZile, ML; Cosper, NJ; Scott, RA; Giedroc, DP (2000)
Biochemistry 39(38), 11818-11829.
10.
"Mechanism of elementary catalytic steps of pyruvate oxidase
from Lactobacillus plantarum"
Tittmann, K; Golbik, R; Ghisla, S; Hubner, G (2000)
Biochemistry 39(35), 10747-10754.
11.
"Dynamic hemicarcerands and hemicarceplexes"
Ro, S; Rowan, SJ; Pease, AR; Cram, DJ; Stoddart, JF (2000)
Org. Lett. 2(16), 2411-2414.
12.
"Interactions of GroEL/GroES with a heterodimeric
intermediate during alpha(2)beta(2) assembly of
mitochondrial branched-chain alpha-ketoacid dehydrogenase -
cis capping of the native-like 86-kDa intermediate by GroES"
Song, JL; Wynn, RM; Chuang, DT (2000)
J. Biol. Chem. 275(29), 22305-22312.
13.
"Alkaline proteinase inhibitor of Pseudomonas aeruginosa -
Interaction of native and N-terminally truncated inhibitor
proteins with Pseudomonas metalloproteinases"
Feltzer, RE; Gray, RD; Dean, WL; Pierce, WM (2000)
J. Biol. Chem. 275(28), 21002-21009.
14.
"Degradation of phytochrome A and the high irradiance
response in Arabidopsis: a kinetic analysis"
Hennig, L; Buche, C; Schafer, E (2000)
Plant Cell Environ. 23(7), 727-734.
15.
"Characteristics of L-ornithine: 2-oxoacid aminotransferase
and potential prenatal diagnosis of gyrate atrophy of the
choroid and retina by first trimester chorionic villus
sampling"
Roschinger, W; Endres, W; Shin, YS (2000)
Clin. Chim. Acta 296(1-2), 91-100.
16.
"Dissecting the nucleotide binding properties of Escherichia
coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
with fluorescent 3 '(2)'-o-anthraniloyladenosine 5
'-triphosphate"
Shi, GB; Gong, YC; Savchenko, A; Zeikus, JG; Xiao, B; Ji,
XH; Yan, HG (2000)
Biochim. Biophys. Acta-Protein Struct. Molec. Enzym.
1478(2), 289-299.
17.
"Mechanism of neomycin and Rev peptide binding to the Rev
responsive element of HIV-1 as determined by fluorescence
and NMR spectroscopy"
Lacourciere, KA; Stivers, JT; Marino, JP (2000)
Biochemistry 39(19), 5630-5641.
18.
"Transient kinetics of ligand binding and role of the
C-terminus in the dUTPase from equine infectious anemia
virus"
Nord, J; Kiefer, M; Adolph, HW; Zeppezauer, MM; Nyman, PO
(2000)
FEBS Lett. 472(2-3), 312-316.
19.
"A novel approach to serine protease inhibition: Kinetic
characterization of inhibitors whose potencies and
selectivities are dramatically enhanced by zinc(II)"
Janc, JW; Clark, JM; Warne, RL; Elrod, KC; Katz, BA; Moore,
WR (2000)
Biochemistry 39(16), 4792-4800.
20.
"Structural basis for selectivity of a small molecule, S1-
binding, submicromolar inhibitor of urokinase-type
plasminogen activator"
Katz, BA; Mackman, R; Luong, C; Radika, K; Martelli, A;
Sprengeler, PA; Wang, J; Chan, HD; Wong, L (2000)
Chem. Biol. 7(4), 299-312.
21.
"Osmotic pressure effects on EcoRV cleavage and binding"
Wenner, JR; Bloomfield, VA (1999)
J. Biomol. Struct. Dyn. 17(3), 461-471.
22.
"GroEL/GroES promote dissociation/reassociation cycles of a
heterodimeric intermediate during alpha(2)beta(2) protein
assembly - Iterative annealing at the quaternary structure
level"
Wynn, RM; Song, JL; Chuang, DT (2000)
J. Biol. Chem. 275(4), 2786-2794.
23.
"Hydrophilic residues at the apical domain of GroEL
contribute to GroES finding but attenuate polypeptide
binding"
Motojima, F; Makio, T; Aoki, K; Makino, Y; Kuwajima, K;
Yoshida, M (2000)
Biochem. Biophys. Res. Commun. 267(3), 842-849.
24.
"Kinetic modelling in food science: a case study on
chlorophyll degradation in olives"
van Boekel, MAJS (2000)
J. Sci. Food Agric. 80(1), 3-9.
25.
"Microcomputer applications in biochemistry"
Tsai, CS (2000)
J. Chem. Educ. 77(2), 219-221.
26.
"Crowding effects on EcoRV kinetics and binding"
Wenner, JR; Bloomfield, VA (1999)
Biophys. J. 77(6), 3234-3241.
27.
"Selective antibody-catalyzed solvolysis of endo-2-norbornyl
mesylate"
Ma, LF; Sweet, EH; Schultz, PG (1999)
J. Am. Chem. Soc. 121(43), 10227-10228.
28.
"Substrate channeling"
Spivey, HO; Ovadi, J (1999)
Methods 19(2), 306-321.
29.
"Testing of kinetic models: usefulness of the multiresponse
approach as applied to chlorophyll degradation in foods"
van Boekel, MAJS (1999)
Food Res. Int. 32(4), 261-269.
30.
"Role of electrophilic and general base catalysis in the
mechanism of Escherichia coli uracil DNA glycosylase"
Drohat, AC; Jagadeesh, J; Ferguson, E; Stivers, JT (1999)
Biochemistry 38(37), 11866-11875.
31.
"Rate determination in phosphorylation of shark rectal Na,K-
ATPase by ATP: Temperature sensitivity and effects of ADP"
Cornelius, F (1999)
Biophys. J. 77(2), 934-942.
32.
"Adenylosuccinate synthase from Saccharomyces cerevisiae:
homologous overexpression, purification and characterization
of the recombinant protein"
Lipps, G; Krauss, G (1999)
Biochem. J. 341(Pt. 3), 537-543.
33.
"Synthesis and biochemical evaluation of
bis(6,7-dimethyl-8-D- ribityllumazines) as potential
bisubstrate analogue inhibitors of riboflavin synthase"
Cushman, M; Mavandadi, F; Yang, DL; Kugelbrey, K; Kis, K;
Bacher, A (1999)
J. Org. Chem. 64(13), 4635-4642.
34.
"The propeptides of the vitamin K-dependent proteins possess
different affinities for the vitamin K-dependent
carboxylase"
Stanley, TB; Jin, DY; Lin, PJ; Stafford, DW (1999)
J. Biol. Chem. 274(24), 16940-16944.
35.
"Design, synthesis, and biological evaluation of homologous
phosphonic acids and sulfonic acids as inhibitors of
lumazine synthase"
Cushman, M; Mihalic, JT; Kis, K; Bacher, A (1999)
J. Org. Chem. 64(11), 3838-3845.
36.
"Reactions of prostaglandin endoperoxide synthase with
hydroperoxide and reducing substrates under single turnover
conditions"
Koshkin, V; Dunford, HB (1999)
Biochim. Biophys. Acta-Protein Struct. Molec. Enzym.
1431(1), 47-52.
37.
"RXP 407, a phosphinic peptide, is a potent inhibitor of
angiotensin I converting enzyme able to differentiate
between its two active sites"
Dive, V; Cotton, J; Yiotakis, A; Michaud, A; Vassiliou, S;
Jiracek, J; Vazeux, G; Chauvet, MT; Cuniasse, P; Corvol, P
(1999)
Proc. Natl. Acad. Sci. U. S. A. 96(8), 4330-4335.
38.
"Coupling of the peroxidase and cyclooxygenase reactions of
prostaglandin H synthase"
Koshkin, V; Dunford, HB (1999)
Biochim. Biophys. Acta-Protein Struct. Molec. Enzym.
1430(2), 341-348.
39.
"Buffer effects on EcoRV kinetics as measured by fluorescent
staining and digital imaging of plasmid cleavage"
Wenner, JR; Bloomfield, VA (1999)
Anal. Biochem. 268(2), 201-212.
40.
"Superoxide free radical generation by Amadori compounds:
The role of acyclic forms and metal ions"
Mossine, VV; Linetsky, M; Glinsky, GV; Ortwerth, BJ;
Feather, MS (1999)
Chem. Res. Toxicol. 12(3), 230-236.
41.
"Crystal structure of Escherichia coli uracil DNA
glycosylase and its complexes with uracil and glycerol:
Structure and glycosylase mechanism revisited"
Xiao, GY; Tordova, M; Jagadeesh, J; Drohat, AC; Stivers, JT;
Gilliland, GL (1999)
Proteins 35(1), 13-24.
42.
"Kinetic mechanism of damage site recognition and uracil
flipping by Escherichia coli uracil DNA glycosylase"
Stivers, JT; Pankiewicz, KW; Watanabe, KA (1999)
Biochemistry 38(3), 952-963.
43.
"Studies on the catalysis of carbon-cobalt bond homolysis by
ribonucleoside triphosphate reductase: Evidence for
concerted carbon-cobalt bond homolysis and thiyl radical
formation"
Licht, SS; Booker, S; Stubbe, JA (1999)
Biochemistry 38(4), 1221-1233.
44.
"General numerical treatment of competitive binding
kinetics: Application to thrombin-dehydrothrombin-hirudin"
Kuzmic, P (1999)
Anal. Biochem. 267(1), 17-23.
45.
"Non-linear optimization of biochemical pathways:
applications to metabolic engineering and parameter
estimation"
Mendes, P; Kell, DB (1998)
Bioinformatics 14(10), 869-883.
46.
"E2P phosphoforms of Na,K-ATPase. II. Interaction of
substrate and cation-binding sites in P-i phosphorylation of
Na,K-ATPase"
Cornelius, F; Fedosova, NU; Klodos, I (1998)
Biochemistry 37(47), 16686-16696.
47.
"Stability of recombinant yeast protoporphyrinogen oxidase:
Effects of diphenyl ether-type herbicides and
diphenyleneiodonium"
Arnould, S; Takahashi, M; Camadro, JM (1998)
Biochemistry 37(37), 12818-12828.
48.
"Spectroscopic characterization of intermediates in the
urate oxidase reaction"
Kahn, K; Tipton, PA (1998)
Biochemistry 37(33), 11651-11659.
49.
"Antibody catalysis of peptidyl-prolyl cis-trans
isomerization in the folding of RNase T1"
Ma, LF; Hsieh-Wilson, LC; Schultz, PG (1998)
Proc. Natl. Acad. Sci. U. S. A. 95(13), 7251-7256.
50.
"Kinetic determinations and some kinetic aspects of
analytical chemistry"
Crouch, SR; Cullen, TF; Scheeline, A; Kirkor, ES (1998)
Anal. Chem. 70(12), 53R-106R.
51.
"Fixed-point methods for computing the equilibrium
composition of complex biochemical mixtures"
Kuzmic, P (1998)
Biochem. J. 331(Pt. 2), 571-575.
52.
"Regulation of extrinsic pathway factor Xa formation by
tissue factor pathway inhibitor"
Baugh, RJ; Broze, GJ; Krishnaswamy, S (1998)
J. Biol. Chem. 273(8), 4378-4386.
53.
"Design of potent selective zinc-mediated serine protease
inhibitors"
Katz, BA; Clark, JM; Finer-Moore, JS; Jenkins, TE; Johnson,
CR; Ross, MJ; Luong, C; Moore, WR; Stroud, RM (1998)
Nature 391(6667), 608-612.
54.
"Structure-based thermodynamic design of peptide ligands:
Application to peptide inhibitors of the aspartic protease
endothiapepsin"
Luque, I; Gomez, J; Semo, N; Freire, E (1998)
Proteins 30(1), 74-85.
