<p><strong>Cyclodextrin Guest Analysis Tool (CDGA)</strong></p><p>This entry contains two workflows for the investigation of native cyclodextrin complexes. The workflows allow comparison of guest molecules located inside the cyclodextrin cavity. Aligned and non-aligned complexes are exported as MOL files for further visualization. The script also generates the matching atom list used for RMSD calculation.</p><ol><li><p><strong>Cyclodextrin Guest Analysis Align Tool (CDGA Align)<em> - </em></strong><em>Workflow WITH alignment of cyclodextrin complexes:</em></p><ul><li><p>This workflow first aligns all complexes based only on the cyclodextrin structure. After alignment, the script calculates descriptors describing the position and orientation of the guest molecule inside the cyclodextrin cavity.</p></li><li><p>The calculated descriptors include:</p><ul><li><p>Depth of the guest in the cavity</p></li><li><p>Angle relative to the cyclodextrin axis</p></li><li><p>Guest orientation</p></li><li><p>Heavy-atom RMSD relative to the reference complex.</p><p></p></li></ul></li></ul></li><li><p><strong><em>Cyclodextrin Guest Analysis NoAlign Tool (CDGA NoAlign) - </em></strong>Workflow WITHOUT alignment of cyclodextrin complexes:</p></li></ol><p>This workflow calculates the same descriptors for the guest molecule inside the cyclodextrin cavity but<strong> does not perform alignment of the complexes.</strong></p><p>This option is useful when the complexes have already been aligned beforehand using other tools or software. The workflow then calculates the structural properties of the guest molecule relative to the reference complex.</p><p>----------------------------------------------------------------------------</p><p>The <strong>Host Characterization</strong> module provides additional information about the conformation of the cyclodextrin host for CDGA Align and NoAlign workflows.</p><p>The exported XYZ coordinates of pyranoze atoms can be used as input for external analyses of pyranose ring conformation, including Cremer Pople puckering analysis. The module also calculates the glycosidic torsion angles φ and ψ for every linkage between consecutive pyranose units.</p><p>-------------------------------------------------------------------------------</p><p>This workflow is distributed under the GNU General Public License v3.0 (GPL-3.0). Third-party software, libraries, KNIME extensions and data remain subject to their respective license terms and are not covered by the CDGA license unless explicitly stated otherwise.</p><p></p><p>The User Manual, test data files and more details for CDGA Tool can be found in the accompanying GitHub Repository.</p><p></p><p>Users should review the applicable license terms before installing, executing, modifying, or redistributing the CDGA Tool and its associated data.</p><p></p><p>If you use CDGA Tool in a published work, please cite the following publication:</p><p>Ewa Napiórkowska, Łukasz Szeleszczuk; CDGA: A Host-Based Alignment and Descriptor Analysis Tool for Cyclodextrin Inclusion Complexes. <em>J. Chem. Inf. Model.</em> 2026; https://doi.org/10.1021/acs.jcim.6c02866</p><p>--------------------------------------------------------------------------------</p><p>CDGA uses MOL files as input. To support PDB structures, including multiframe PDB files, a separate conversion workflow is provided.</p>