Sentence examples for binding poses and are from inspiring English sources

The medoids of the clusters obtained are considered as representative binding poses and are used as starting configurations for the MD simulations of the ligand-protein complex.

There is only one case where the free energy calculations appear to be unable to unambiguously identify the most stable binding pose and that is ligand 6.

The main purpose of a scoring function though is to rank binding poses, and here the MOE scoring functions are effective.

During the docking analysis, the ligand was represented by an all-atom model and considered fully flexible in the potential field of the receptor, and the binding pose and internal torsions were sampled by the biased probability Monte Carlo (BPMC) minimization procedure, which involved local energy minimization after each random move.

Incorporating conformational rearrangements of the receptor binding pocket into predictions of both ligand binding pose and binding score is crucial for improving structure-based drug design and virtual ligand screening methodologies.

In the framework of the 2015 D3R inaugural grand challenge, blind binding pose and affinity predictions were performed for a set of 180 ligands of the Heat Shock Protein HSP90-α protein, a relevant cancer target.

The pharmacophore-based pose sampling and ranking scheme was deployed to efficiently filter out ligand binding poses that are unlikely to be the native binding pose.

In computational docking, a large number of binding poses are evaluated and ranked using a scoring function.

In this process, a large number of binding poses are computationally generated and then evaluated using a scoring function (SF), which is a mathematical or predictive model that produces a score representing binding stability of the pose.

Fig. 3 5c, 5c and 5f between Cys 813 and Tyr 802 of binding pocket (a) their binding poses are same and are overlapping with each other.

The apelin and MM07-apelin receptor binding poses are shown in Figure 1 taken from the most representative structure of the principal cluster of the MD simulation trajectory.