webZyme realistically simulates kinetics experiments. A new enzyme is like a black box - it obeys rules, dictated by the mechanism, that are
unknown to the enzymologyst; experiments uncover these rules/deduce the mechanism. Similarly, webZyme returns the results of experiments defined by the user; these results are calculated
by the equations - unknown to the student-user - that were derived from the mechanism entered by the professor.
webZyme currently simulates:
Absorbance stopped-flow experiments - The professor defines absorbance spectra, sets the noise level, and selects
the enzyme forms and reagents that are available. The student specifies the contents of the stopped-flow instrument, the
wavelength to observe, and the schedule for collecting data-points.
Fluorescence stopped-flow experiments - The professor defines the excitation spectra (same as absorbance spectra), the emission spectra,
the noise level, and selects the enzyme forms and reagents that are available. The student specifies the contents of the
stopped-flow instrument, the wavelength to observe, and the schedule for collecting data-points.
Chemical quenching - The professor selects which species will survive the quench and which species in the mechanism
contribute to this. The student selects the reaction time.
Steady-state velocities - The professor designates which species in the mechanism are enzyme forms and sets the noise-
level. The student enters the concentrations of substrates and enzyme.
...a data analysis program. webZyme is not a curve-fitting program. The results generated by webZyme should be
exported to your favorite curve-fitting program for analysis.
...a substitute for standard simulation programs. KINSIM, Berkeley Madonna, Gepasi, etc. are excellent tools for simulating
the results of a mechanism and experiment whose every detail you already know, or wish to postulate. webZyme withholds
the underlying information, requiring discovery.
...expensive. Use our server for free - just send Bruce an e-mail.
...finished. Features are still being added, and bugs are still being found (and fixed).
This is a brief description of an older version
This is a poster describing an older version
This is a poster describing the new version
The current version does much more, and someday we'll have complete documentation.