Construction and visualization of transition pathways

The SmoothT software offers the construction of transition pathways from a zipped ensemble of conformations. The user provides an archive of molecule conformations in PDB format, from which a starting and a final conformation need to be selected. The individual PDB files need to contain an energy value or score, estimating the quality of the respective conformation. Additionally, the user has to provide a RMSD cutoff, below which conformations are considered neighboring. From this SooothT constructs a graph that connects similar conformations. SmoothT returns the energetically most favorable pathway within in this graph. This pathway is directly displayed as interactive animation using the NGL viewer. Simultaneously, the energy along the pathway is plotted, highlighting the conformation that is currently displayed in the 3D window.

Ensembles up to 2 GB (compressed) can be uploaded. For large zip files approaching 2GB, expect 3-12 minutes of runtime (assuming there are no other jobs in the queue), split fairly evenly between upload, unpacking, and pathway calculation. Results will be stored for 5 days.

The C++ source code is available for download at:


download test data

Settings creating the default example:

upload: downloaded zip file
start structure: 5c1m_FullAnalysis_19_29_09_2021_score7_2_8_13_16_0001.pdb
final structure: 5c1m_FullAnalysis_15_28_09_2021_cluster4_4_0001.pdb
chain: X
rmsd cutoff: 5.0
energy identifyer: total_score