Literature DB >> 6688159

Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM--a flexible, portable system.

B A Barshop, R F Wrenn, C Frieden.   

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.

Mesh:

Year:  1983        PMID: 6688159     DOI: 10.1016/0003-2697(83)90660-7

Source DB:  PubMed          Journal:  Anal Biochem        ISSN: 0003-2697            Impact factor:   3.365


  100 in total

1.  DNA specificity enhanced by sequential binding of protein monomers.

Authors:  J J Kohler; S J Metallo; T L Schneider; A Schepartz
Journal:  Proc Natl Acad Sci U S A       Date:  1999-10-12       Impact factor: 11.205

2.  Characterization of the hinges of the effector loop in the reaction pathway of the activation of ras-proteins. Kinetics of binding of beryllium trifluoride to V29G and I36G mutants of Ha-ras-p21.

Authors:  S Kuppens; J F Díaz; Y Engelborghs
Journal:  Protein Sci       Date:  1999-09       Impact factor: 6.725

3.  Kinetics studies of the cardiac Ca-ATPase expressed in Sf21 cells: new insights on Ca-ATPase regulation by phospholamban.

Authors:  J E Mahaney; J M Autry; L R Jones
Journal:  Biophys J       Date:  2000-03       Impact factor: 4.033

4.  An essential intermediate in the folding of dihydrofolate reductase.

Authors:  D K Heidary; J C O'Neill; M Roy; P A Jennings
Journal:  Proc Natl Acad Sci U S A       Date:  2000-05-23       Impact factor: 11.205

5.  Folding of a three-stranded coiled coil.

Authors:  E Dürr; H R Bosshard
Journal:  Protein Sci       Date:  2000-07       Impact factor: 6.725

6.  Understanding the kinetic roles of the inducer heparin and of rod-like protofibrils during amyloid fibril formation by Tau protein.

Authors:  Gayathri Ramachandran; Jayant B Udgaonkar
Journal:  J Biol Chem       Date:  2011-09-19       Impact factor: 5.157

7.  Use of experimental isotope-exchange fluxes in reversible enzyme and membrane transport models, assessed by simultaneous computer simulation of unidirectional and net chemical rates.

Authors:  I W Plesner
Journal:  Biochem J       Date:  1992-08-15       Impact factor: 3.857

8.  The control of actin nucleotide exchange by thymosin beta 4 and profilin. A potential regulatory mechanism for actin polymerization in cells.

Authors:  P J Goldschmidt-Clermont; M I Furman; D Wachsstock; D Safer; V T Nachmias; T D Pollard
Journal:  Mol Biol Cell       Date:  1992-09       Impact factor: 4.138

9.  Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA.

Authors:  Arnon Henn; Wenxiang Cao; Nicholas Licciardello; Sara E Heitkamp; David D Hackney; Enrique M De La Cruz
Journal:  Proc Natl Acad Sci U S A       Date:  2010-02-16       Impact factor: 11.205

10.  Role of a GAG hinge in the nucleotide-induced conformational change governing nucleotide specificity by T7 DNA polymerase.

Authors:  Zhinan Jin; Kenneth A Johnson
Journal:  J Biol Chem       Date:  2010-10-26       Impact factor: 5.157

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