One of the ultimate goals in drug discovery and design is to computationally screen many drug candidates to the biological target molecules and is to find the most plausible binding mode as well as binding strength using different strategies such as molecular docking, MD simulations and free energy calculations. For instance, in molecular docking both search algorithms and scoring functions are limited to the attempts the software makes during the docking process. Hence, the conformer generation prior to docking can improve both search and scoring efficiency by creating a good starting structure. For this reason, most conformer generation algorithms are assessed for their performance on finding the bioactive conformations. In this step, we assess the performance of auto3d and DeepConf to reproduce the bioactive conformations in the absence of target biomolecule. We have followed a unique protocol which can be a guideline for benchmarking conformer generation algorithms' performance to capture the bioactive conformation.