Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM--a flexible, portable system
- PMID: 6688159
- DOI: 10.1016/0003-2697(83)90660-7
Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM--a flexible, portable system
Abstract
A flexible and convenient computational method for the simulation of kinetic progress curves has been developed. A mechanism is represented in conventional chemical format with either kinetic or rapid equilibrium steps separating chemical species. A table describing the differential equations of the mechanism is generated and a direct numerical integration is performed. The same program can be used to simulate any number of mechanisms. The user may interactively set kinetic parameters to seek the optimal fit for a set of experiments, as determined by graphical superimposition of simulated curves with experimental data. Standard error analysis and automatic optimization may also be included. The program is computationally efficient and its interactive nature makes it a good teaching tool. The source code is written in FORTRAN IV and adheres closely with the ANSI 1966 standard, so as to make it maximally portable and machine independent.
Similar articles
-
Analysis of progress curves by simulations generated by numerical integration.Biochem J. 1989 Mar 1;258(2):381-7. doi: 10.1042/bj2580381. Biochem J. 1989. PMID: 2705989 Free PMC article.
-
A program for the numerical integration of enzyme kinetic equations using small computers.Int J Biomed Comput. 1984 Nov-Dec;15(6):419-32. doi: 10.1016/0020-7101(84)90013-8. Int J Biomed Comput. 1984. PMID: 6548981
-
A set of programs for analysis of kinetic and equilibrium data.Comput Appl Biosci. 1990 Jul;6(3):213-21. doi: 10.1093/bioinformatics/6.3.213. Comput Appl Biosci. 1990. PMID: 2207745
-
Fitting enzyme kinetic data with KinTek Global Kinetic Explorer.Methods Enzymol. 2009;467:601-626. doi: 10.1016/S0076-6879(09)67023-3. Methods Enzymol. 2009. PMID: 19897109 Review.
-
New PC versions of the kinetic-simulation and fitting programs, KINSIM and FITSIM.Trends Biochem Sci. 1997 Aug;22(8):317. doi: 10.1016/s0968-0004(97)01062-1. Trends Biochem Sci. 1997. PMID: 9270307 Review. No abstract available.
Cited by
-
Dimeric Eg5 maintains processivity through alternating-site catalysis with rate-limiting ATP hydrolysis.J Biol Chem. 2006 Dec 22;281(51):39444-54. doi: 10.1074/jbc.M608056200. Epub 2006 Oct 23. J Biol Chem. 2006. PMID: 17062577 Free PMC article.
-
Kinetics studies of the cardiac Ca-ATPase expressed in Sf21 cells: new insights on Ca-ATPase regulation by phospholamban.Biophys J. 2000 Mar;78(3):1306-23. doi: 10.1016/S0006-3495(00)76686-0. Biophys J. 2000. PMID: 10692318 Free PMC article.
-
Mechanism of Substrate Recognition and Catalysis of the Haloalkanoic Acid Dehalogenase Family Member α-Phosphoglucomutase.Biochemistry. 2018 Jul 31;57(30):4504-4517. doi: 10.1021/acs.biochem.8b00396. Epub 2018 Jul 13. Biochemistry. 2018. PMID: 29952545 Free PMC article.
-
Formation of metastable RNA structures by sequential folding during transcription: time-resolved structural analysis of potato spindle tuber viroid (-)-stranded RNA by temperature-gradient gel electrophoresis.RNA. 1999 Apr;5(4):574-84. doi: 10.1017/s1355838299982018. RNA. 1999. PMID: 10199573 Free PMC article.
-
Kinetic analysis of the guanine nucleotide exchange activity of TRAPP, a multimeric Ypt1p exchange factor.J Mol Biol. 2009 Jun 5;389(2):275-88. doi: 10.1016/j.jmb.2009.03.068. Epub 2009 Apr 8. J Mol Biol. 2009. PMID: 19361519 Free PMC article.
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources