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The time course data were fitted by iterative simulation using the KinTek Corp. Global Kinetic Explorer software program.
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The iterative simulation used the tool SOLVER in Excel 2003 (Microsoft, Redmond, WA, USA).
The time course for the single-turnover reaction was fitted by iterative curve simulation using the reaction sequence YdiI + benzoyl-CoA ↔ YdiI·(benzoyl-CoA) → YdiI·(CoA)(benzoic acid) in conjunction with the KinTek Corporation Global Kinetic Explorer software to define the benzoyl-CoA kon = 50 125 μM–1·s–1 and koff = 400 650 s–1, and for the chemical step(s) kobs = 15 19 s 1.
Draft assemblies were extended by iterative mapping using IMAGE [ 29] and corrected using iCORN2 [ 30].
Sixty of those were resolved by iterative mapping using our data set.
Several rounds of initial refinement were carried out using REFMAC5, accompanied by iterative model building using COOT.
In the future, lattice strain could be incorporated in simulations using an iterative approach, involving an initial comparison with simulations to obtain a first estimate of the composition, followed by comparison with a new model that incorporates relaxation of the structure.
Individual competition binding experiments were analyzed by iterative curve fitting using Prism.
The process of PIP2 lipid segregation near STX was modeled with an iterative approach combining all-atom MD simulations with mesoscale simulations using the self-consistent mean-field model, CGM, that we have formulated and implemented as described previously.
This approach uses an iterative simulation scheme, so that the model need not be resolved analytically (see [30] for an introduction to MCMC techniques in ecology).
This was achieved by an iterative process using the.cel file parser script.
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