Sentence examples for binding pockets were predicted from inspiring English sources
Five potential binding pockets were predicted as shown in Figure 2a.
Cavities surrounding the core of the GABA binding pocket were predicted by molecular interaction field calculations and docking studies in a α1β2γ2 GABAA receptor homology model, and were confirmed by affinities of substituted analogues of 3. The tight steric requirements observed for the remarkably few GABAAR agonists reported to date is challenged by our findings.
Gunasekaran and Nussinov reported that the magnitude of the dihedral angle changes is minimal after ligand binding [ 19], which explains why our method has a performance similar to that of Ligsite-csc for both ligand-bound and ligand-free protein ligand-binding site prediction when only one potential pocket is predicted, as shown in Figure 6.
Binding pockets are correctly predicted in 94% and 93% of the datasets.
The phenylalanine pocket is predicted to be important for ligand binding,[ 51] and running Q-SiteFinder,[ 10] ANCHOR[ 9] and Dr PIAS[ 7, 8] on the RAD51 BRC4 structure identified the phenylalanine pocket as a high-scoring binding site.
To answer this question we developed a panel of peptides designed so that amino acids interacting with the p6 and p9 predicted MHC binding pockets were altered.
The predicted interacting residues obtained by AutoDock were matched with the predicted binding pocket amino acids of metaPocket finder and Q-site finder, and these binding pockets were referred for docking in FlexX and GOLD.
Binding-pocket volumes were predicted using Pocket Finder (Molsoft ICM 3.7-d).
Amino acid residues that are located in or near predicted binding pockets are likely to alter the binding capability for ligand(s).
We present the 2.8 Å crystal structure of GTP-bound L129F mutant Rab7 which reveals normal conformations of the effector binding regions and catalytic site, but an alteration to the nucleotide binding pocket that is predicted to alter GTP binding.
S163 is located below the binding pocket and was predicted to be <5 Å from palonosetron in the allosteric site proposed by Moura Barbosa et al., but not directly involved in its binding.
