A third approach has used error minimization algorithms to predict scale structures under the assumption of competing preferences for small integer ratios and equal intervals between successive scale tones [15], [16].
Thermodynamic processes with free energy parameters are often used in algorithms that solve the free energy minimization problem to predict secondary structures of single RNA sequences.
Therefore, beyond the static view of RNA folding using energy minimization methods to predict the final state of the folding, a time-dependent view is desired in order to extract information on the folding kinetics.
We will use logic minimization techniques to predict the TFBS for the transcription factor SOX9, which is a member of the SOX protein family that play critical roles in the regulation of numerous developmental processes, including sex determination, skeleton formation, pre-B and T-cell development and neural induction [ 10].
Consequently, a molecular mechanics approach, using potential energy minimization, was employed to predict the conformation of aldehyde 6 in the minor groove of the DNA duplex.
An energy minimization framework is employed to predict the actuation force on a droplet.
In addition we used in situ ligand minimization in an attempt to predict the mode of binding of the DOTA-conjugated HtBv agent 9 to its protein targets.
Using an energy minimization approach, we were able to predict the number of folds in this regularly folded conformation.
In order to have an estimate of the production rate for each case, we used the method of minimization of metabolic adjustment (MOMA) to predict the flux distribution of the mutants (Segrè et al., 2002).
The OPM database (Orientations of Proteins in Membranes; Lomize et al., 2006a) applies minimization of a free energy expression to predict the transmembrane part of a protein structure.
