Specify the temperature: The Foldeomics Consortium recommends to set the temperature in your experiments at 25°C, but you can enter any other value (larger than 0 Kelvin, that is). Other recommendations of experimental conditions can be found in Maxwell et. al. (2005), Protein Folding: Defining a Standard Set of Experimental Conditions and a Preliminary Kinetic Data Set of Two-State Proteins, Protein Science, 14(3): 602-16.

Specify the energy units: Some parameter estimates concern energies such as ΔΔG_U and ΔΔG_‡. You can select whether you want the units in kJ or kcal.

Specify the comparisons: If you are only interested in Φ-values concerning wildtype versus mutant comparisons, check the wildtype only radio button. In this case, it is assumed that the data for the wildtype are in the first two columns (denaturant concentration and folding rates, respectively). All comparisons are carried out with respect to that chevron. If you want to consider all pairwise comparisons between chevron curves, check the all comparisons radio button. The results will also include double mutants if you supply data obtained from mutations at different sequence locations. If those are not your cup of tea, you can simply delete them in the spread sheet returned to you.

Specify the type of fit: Check the parallel arms radio button if you want to fit the same m_f and the same m_u in all chevrons. That means, you restrict all all folding arms to be parallel, and all unfolding arms to be parallel. Check the individual chevron fit radio button if you want to allow for different slopes, i.e. fit individual chevron curves.

Specify the denaturant concentrations: This is only relevant if you choose to fit individual chevron curves. Some folks prefer estimating the kinetic parameters at positive concentrations of denaturant (even though, unless the folding and unfolding arms are parallel, they measure something different then). If you you are one of those guys, you can type in any non-negative number for the folding rate and the unfolding rate.

Specify the coverage for the Φ-value confidence intervals: All uncertainties are given as standard errors. For the Φ-value however, a confidence interval is also given. The default is 95% coverage, but you can specify any other confidence level (larger than 0%, but smaller than 100%).

Specify the number of significant digits in the output: The estimates and standard errors are returned as tables on a webpage in html format, and also as spreadsheets easily read into slides or other documents. You can specify the number of significant digits (number of digits after the dot) in those tables. The default is 2.

Output: Ther Perl and R scripts generate a website that contains a table with kinetic parameter estimates and their respective standard errors, and a table with the estimates for the Φ-values, changes of free energy, etc. Note that every estimate will be returned, even if it is obviously not meaningful (such as Φ-value estimates with huge standard errors). There will be links on the webpage that allow for downloading those tables in spread sheet (csv) format (which then can easily be read into Excel or R), and the user can edit those tables to his or her likings. Some graphical representation of the data will also be provided. An example of such an output page is here.

If you find a bug, or have questions/suggestions, please send me an email. Thanks!