Sentence examples for binding poses using the from inspiring English sources

In this protocol, the receptor structure is held rigid and the estradiol is free to rotate and explore most probable binding poses using the Lamarckian genetic algorithm.

In the default setting, PharmDock searches the ligand binding poses using all protein-based pharmacophores independent from information about known active ligands.

A consideration of the optimal binding pose for the modelled ligands was out of the scope of this work, and further validations regarding conformational refinement of docked or aligned poses using the FMO method are in progress.

Sketch the pose using the wireframe as a guide.

The resulting binding poses were scored using the Hawkins GB/SA function of DOCK 6.

For each compound up to 10 binding poses were ranked using the Chemgauss 4 scoring function.

All binding poses were evaluated using the DOCK grid-based scoring, involving the non-bonded terms of the AMBER molecular mechanics force field (vDW+ES).

A total of 106 protein-halogenated ligand complexes were tested and compared in terms of binding affinity and docking poses using Vina and VinaXB.

Poses with RMSD<3.0 Å were energy-minimized in the protein binding cleft using the MMFF94x force field in MOE.

Our scoring method consists of two steps: predicting the binding poses of ligands using a docking program, and then refining and rescoring those protein-ligand complexes using a more computationally intensive molecular-mechanics based energy function.

In our previous study, we have presented pose prediction and ranking results using pharmacophore models without any local optimization of the binding poses or use of an atomistic scoring function.