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The recent rise of cryo-EM and X-ray high-throughput techniques is providinga wealth of new structures trapped in different conformations. Understandinghow proteins transition between different conformers, and how they relate toeach other in terms of function is not straightforward, and highly depends onthe choice of the right set of degrees of freedom. Here we present eBDIMSserver, an online tool and software for automatic classification of structuralensembles and reconstruction of transition pathways using coarse-grained (CG)simulations. The server generates CG-pathways between two protein conformationsalong with a representation in a simplified 2D-motion landscape based on thePrincipal Components (PCs) from experimental structures. For a conformationallyrich ensemble, the PCs provide powerful reaction coordinates for automaticstructure classification, detection of on-pathway intermediates and validationof in silico pathways. When the number of available structures is low orsampling is limited, Normal Modes (NMs) provide alternative motion axes fortrajectory analysis. The path-generation eBDIMS method is available at auser-friendly website: https://login.biophysics.kth.se/eBDIMS/ or as standalonesoftware. The server incorporates a powerful interactive graphical interfacefor simultaneous visualization of transition pathways in 2D-motion space and3D-molecular graphics, which greatly facilitates the exploration of therelationships between different conformations.

The eBDIMS path-sampling server: generation, classification and  interactive visualization of protein ensembles and transition pathways in  2D-motion space