The correlation between PharmDock's predicted binding energies with the experimentally measured binding affinities was used to evaluate PharmDock's performance in binding energy estimation.
A hierarchy of binding affinities was used, based on the in vitro experiments (Brittle et al., 2010; Simon et al., 2010), with phosphorylated Ft (FtP) and unphosphorylated Ds (Ds) producing the strongest partnership, and unphosphorylated Ft (Ft) and phosphorylated Ds (DsP) producing the weakest partnership (see 'Materials and methods').
For each data point, the input to the neural network is a sequence consisting of 43 peptide-HLA residues (9 from the peptide and 34 from the HLA), and as output the corresponding binding affinity was used.
Region-specific binding affinities were analyzed using Student's unpaired t-test.
The resulting QSAR models for rat and human H3 binding affinities were validated using different strategies.
In this study, a 3D pharmacophore was generated for a set of LAT1 substrates whose binding affinities were studied using competitive inhibition of the brain uptake of [14C]-l-leucine with an in situ rat brain perfusion method.
cprotein binding affinities were obtained using Eq. 6. dsum of the values of the Taft steric parameters of R1and R2. esum of the values of the Taft electronic parameters of R1and R1and
Peptide binding affinities were predicted using a linear combination of the hydrophobic, entropic, and electrostatic components of the interaction free energy with optimized weights.
All apparent binding affinities were obtained using the software BIAevaluation v. 2.2.4 (Biacore, GE Healthcare, Chalfont St. Giles, GB).
The binding affinities were determined using isolated receptor binding assays where the different integrins (α5 β1, α v β3, and α IIb β3) were immobilised and [I]echistatin was replaced by increasing amounts of the different peptides tested.
