SmoothT—a server constructing low-energy pathways from conformational ensembles for interactive visualization and enhanced sampling

• DOI: 10.1093/bioinformatics/btad176
• Publication Date: 2023-04-05T17:03:31Z
• Authors: René Staritzbichler; Nikola Ristic; Tülin Stapke; Peter W Hildebrand
• Keywords: Upload; Graphical user interface

The SmoothT software and webservice offers the construction of pathways from an ensemble conformations. user provides archive molecule conformations in Protein Databank (PDB) format, which a starting final conformation need to be selected. individual PDB files contain energy value or score, estimating quality respective confirmation. Additionally, has provide root-mean-square deviation (RMSD) cut-off, below are considered neighboring. From this, constructs graph that connects similar conformations.SmoothT returns energetically most favorable pathway within this graph. This is directly displayed as interactive animation using NGL viewer. Simultaneously, along plotted, highlighting currently 3D window.SmoothT available at: http://proteinformatics.org/smoothT. Examples, tutorial, FAQs can found there. Ensembles up 2 GB (compressed) uploaded. Results will stored for 5 days. server completely free requires no registration. C++ source code https://github.com/starbeachlab/smoothT.