Sentence examples for docking methods to from inspiring English sources

The Nfs1-scaffold interactions are predicted by protein docking, thus suggesting that using docking methods to resolve pathway structure might be an adequate method, under similar circumstances.

We subsequently carry out a pseudo-prospective study where we repeat the exercise with traditional docking methods to give the initial poses without using any structural information for the protein ligand complexes.

As is the case for the design of novel pharmaceutical agents, the successful application of docking methods to problems in chemical toxicity depends on the identification and availability of the crystal structures of the macromolecular targets or similar proteins.

In this study, we used computer simulation and computer-based molecular docking methods to further explore the interaction modes of YL529 with the kinase domain of VEGFR-3, and Fig.  1 depicts a possible binding configuration of YL529 with VEGFR-3.

Binding modes of representative structures were analyzed using the docking method to explain the observed disparity in HDAC1 inhibitory activities.

We first investigated the ability of the covalent docking method to recapitulate the crystallographic poses of HAD substrate complexes.

Further, the ability of the docking method to predict activity was validated by correlating the estimated binding energies from Autodock4.2 to experimental IC50 values of ten known COX-2 inhibitors (Positive Controls).

Here, we applied theoretical approaches including the quantum mechanics-based density functional theory (DFT) to calculate the activation energy of the α-carbon radical intermediate formation and the molecular mechanics-based docking method to simulate the substrate binding modes to P450s.

As the rigid-body approach was insufficient to simulate the induced conformational fit upon binding, docking methods started to include strategies to mimic molecular flexibility during the optimization (Bonvin reviewed all the diverse strategies developed to deal with molecular flexibility upon binding during the docking process).

Rosetta Dock has the advantage of using explicit flexibility of the side chains and was shown to be one of the best ranked protein-protein docking methods, according to the CAPRI evaluation [20].

The 3-D structures of the peptide epitopes p509, p524, p530 and p570 were modeled using secondary structure prediction and ab initio modeling methods, and 3-D structures of the interaction of peptide epitopes with I-Ag7 were constructed by molecular docking methods, according to the 3-D crystal structure of MHC II I-Ag7 in complex with p207 (PDB code: 1es0).