Examination of the three-dimensional structure of streptavidin aided by empirical binding free-energy calculations helped us to select mutations at subunit interfaces that dissociate the native tetramer and stabilize the desired dimer.
RNAhybrid [ 34] is an algorithm for short nucleic acid hybridizations (free energy calculation) that uses estimated p-values to determine the significance of a predicted binding site and employs no empirical binding rules when filtering.
The powerful empirical binding data and crystal structures present a unique opportunity for computational studies of peptide inhibition of the p53 MDM2/MDMX interactions.
The empirical binding sequences of the TFs are reported [3], [9] in an extended alphabet (e.g. "rACGCGt" for the transcription factor MBP1) specifying the base preferences or the binding affinities as a set of letters with variable case.
Empirical experience shows however that compounds binding to the aforementioned "core" amino acids alone are not high-affinity inhibitors and need additional sources of affinity, like pockets not naturally engaged by protein partner(s) [ 64].
These empirical results were used to develop an algorithm to predict peptide binding to DR1201.
Empirical data show that mRNA synthesis rate is proportional to the equilibrium probability of RNAP binding to promoters [ 12, 25, 26].
Cholesterol binding to ABCG2.
Antibodies attack antigens by binding to them.
