I will present techniques to find reaction coordinates to be used in conjunction with free energy biasing techniques such as the adaptive biasing force method. This allows for instance to improve the sampling of configurations of complex proteins. However, reaction coordinates are often based on an intuitive understanding of the system, and one would like to complement this intuition or even replace it with automated tools. One appealing tool is autoencoders, for which the bottleneck layer provides a low dimensional representation of high dimensional atomistic systems. I will discuss some mathematical foundations of this method, and present illustrative applications including alanine dipeptide. Some on-going extensions to more demanding systems, namely HSP90, will also be mentioned by Zineb Belkacemi, the PhD student working on this project.