SmoothT

SmoothT constructs simple transition pathways between molecular conformations derived from Protein Data Bank (PDB) ensembles to identify energetically favorable biomolecular transitions.

Key Features:

• Pathway Construction: Constructs a connectivity graph linking similar conformations using root-mean-square deviation (RMSD) to determine neighboring states.
• RMSD Cut-off: Applies a user-defined RMSD cut-off to define which conformations are considered neighbors in the graph.
• Energy Evaluation: Requires each PDB file to include an energy value or score and uses these scores to select the most energetically favorable pathway through the graph.
• Visualization: Produces animations of selected pathways using the NGL viewer and plots energy changes along the pathway, indicating the currently displayed conformation.

Scientific Applications:

• Conformational dynamics: Enables analysis of transitions between molecular states within PDB ensembles to study conformational changes.
• Protein folding and unfolding: Facilitates exploration of folding/unfolding trajectories by identifying energetically favorable routes through conformational space.
• Molecular interactions: Supports investigation of conformational changes relevant to molecular interaction mechanisms.
• Energy landscape analysis: Provides insight into the energy landscape of biomolecular transitions using per-conformation energy scores.

Methodology:

Input is an archive of PDB files containing conformations with associated energy scores and specified start and final conformations; a user-defined RMSD cut-off determines neighbor relationships; a connectivity graph is constructed from the ensemble based on the RMSD criteria and the most energetically favorable pathway is identified using the per-conformation energy scores.