Name

Dock close

Software

OpenBabel 2.3.2
Maestro 2018-3
Prime
Smina Apr 2 2016

System Preparation Parameters

NA

System Preparation Method

NA

Pose Prediction Parameters

OpenBabel - Protonated at pH 5.1
Prime - default
Smina - --exhaustiveness=20

Pose Prediction Method

3D structures were generated from provided SMILES strings at pH 5.1 using OpenBabel. The most similar ligand with known structure for each compound was calculated by Tanimoto score and called the 'close' compound. Conformers for each structure were generated using default Prime settings. Conformers were docked using Smina into the receptor of the 'close' ligand. Poses were the selected manually based on Smina score and similarity to 'close' ligand.

Answer 1

Yes

Answer 2

Yes

Name

Dock close

Software

OpenBabel 2.3.2
Maestro 2018-3
Prime
Smina Apr 2 2016

Parameters

OpenBabel - Protonated at pH 5.1
Prime - default
Smina - --exhaustiveness=20

Method

3D structures were generated from provided SMILES strings at pH 5.1 using OpenBabel. The most similar ligand with known structure for each compound was calculated by Tanimoto score and called the 'close' compound. Conformers for each structure were generated using default Prime settings and then clustered using 'Clustering of Conformers' method in Maestro. Representative structures for each cluster were docked using Smina into the receptor of the 'close' ligand. Compounds were then ranked by best Smina score.

Answer 1

No

Answer 2

No