[ANN] Freeware for biochemical kinetics and equilibria

Petr Kuzmic pkuzmic at biokin.com
Tue May 9 09:16:56 EST 2000


___________________________________________________________
[Volume 4]                            B i o K i n   N E W S
[Number 1]                                        May, 2000
-----------------------------------------------------------
                                 Editor: Petr Kuzmic, Ph.D.

Contents
--------
   1. DynaFit version upgrade
   2. Purpose of program DynaFit
   3. Symbolic notation
   4. Revised documentation
   5. Bibliography
   6. Download DynaFit


1. DynaFit version upgrade
--------------------------
The freeware program DynaFit [P. Kuzmic (1996) Anal. Biochem. 237,
260-173] has been updated to version 3.21 and is now available for
download from the BioKin website.


2. Purpose of program DynaFit
-----------------------------
DynaFit is used for the simulation or statistical analysis (nonlinear
least-squares regression) of chemical, biochemical, and biological
data.  Three types of data can be analyzed: (1) reaction progress in
dependence on time, (2) initial reaction velocity in dependence on
concentrations, and (3) composition at equilibrium in dependence on
concentrations.


3. Symbolic Notation
--------------------
The main advantage of program DynaFit is that the investigator may
describe the chemical or biochemical system in terms of symbolic,
stoichiometric equations.  The program derives the underlying
mathematical model automatically.  For example, interaction of a "slow,
tight" inhibitor of a dimeric enzyme (HIV protease) is described as
follows:

   [mechanism]
      Monomer + Monomer <==> Enzyme       :    k1   k2
      Enzyme + Substrate <==> ReactiveX   :    k3   k4
      ReactiveX --> Enzyme + Product      :    k5
      Enzyme + Inhibitor <==> Complex     :    k6   k7

The names of rate constants (k1, k3, ...) and reacting species
('Monomer', 'Enzyme', ...) are arbitrary.


4. Revised documentation
------------------------
The long awaited DynaFit "Scripting Manual" is now available in the
Adobe PDF format.  It is a 130-page document with indexes and
illustrations, explaining in a systematic fashion the syntax of DynaFit
script files.  Also added to the website is a short visual "Getting
Started" tutorial, showing the analysis of a representative data set
screen-by-screen.

* Links:

  http://www.biokin.com/dynafit/scripting/
  http://www.biokin.com/dynafit/quickstart/


5. Bibliography
---------------
The hyperlinks below take you to several recent journal publications in
which DynaFit has been cited.

* "Microcomputer Applications in Biochemistry"
  Tsai S. (2000) J. Chem. Edu. 77(2), 219.

http://jchemed.chem.wisc.edu/Journal/Issues/2000/feb/abs219.html

* "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 R.M. et al. (2000) J. Biol. Chem. 275(4), 2786.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10644743&dopt=Abstract
 
* "Hydrophilic residues at the apical domain of GroEL contribute to
   GroES binding but attenuate polypeptide binding."
   Motojima F. et al. (2000) Biochem. Biophys. Res. Commun. 267(3),842.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10673379&dopt=Abstract

* "Structural basis for selectivity of a small molecule, S1-binding,
   submicromolar inhibitor of urokinase-type plasminogen activator."
   Katz B.A. et al. (2000) Chem. Biol. 7(4), 299.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10779411&dopt=Abstract


6. Download DynaFit
-----------------------
Download DynaFit 3.21 for Windows95/98/NT or for Macintosh from
http://www.biokin.com/dynafit/.

___________________________________________________________
                       BioKin, Ltd. * Consulting & Software
                          P.O. Box 8336 * Madison, WI 53708
                        (608) 256-4790 * (608) 256-1269 FAX
                    info at biokin.com * http://www.biokin.com





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