Photoactive yellow protein was first discovered in Halorho- dospira halophilia, causing the bacterium to flee potentially DNA-damaging light, and serves as a model system for signaling proteins. Upon absorption of a blue photon, PYP's chromophore undergoes a trans-to-cis isomerization that disrupts the hydrogen bond network in the core of the protein, resulting in a large conformational change and transformation into the signaling state. Because of the timescales involved, conventional molecular dynamics simulation of this system is practically impossible. In addition, due to the short signaling state lifetime, experimental determination of the signaling-state structure is also challenging. Here we use a combination of tools we have developed: A coarse-grain model , an all-atom reconstruction technique , locally scaled diffusion maps , and our most recent technique diffusion map-directed molecular dynamics , to explore the elusive structure of the signaling state of PYP.