CycPeptMPDB-4D: A Conformational Dynamics Dataset of Cyclic Peptides for Membrane Permeability Prediction CycPeptMPDB-4D is a large-scale structural dynamics dataset featuring atomistic molecular dynamics (MD) trajectories and 3D conformational ensembles for 5,160 structurally diverse cyclic peptides. It extends CycPeptMPDB by adding MD-derived conformations and physics-based molecular descriptors. This resource is designed to support the development of 3D and 4D (trajectory- or ensemble-based) deep learning models for predicting membrane permeability, bridging the gap between static 2D representations and the physical mechanisms of peptide–membrane interaction. A key feature of this dataset is the inclusion of simulations in both explicit water and hexane environments. This dual-solvent approach captures the "chameleon-like" behavior of cyclic peptides—their ability to adopt distinct conformational states to maximize stability in aqueous environments and minimize polar exposure in hydrophobic membrane cores. More details can be found here: (Link to be added upon publication) Dataset Structure The data is organized into solvent-specific directories containing structural information and a central metadata file: CycPeptMPDB-4D/├── Water/ 5,160 peptides│ ├── Trajectories/ *.pdb (100 frames per peptide)│ ├── Structures/ Representative conformations from clustering│ └── Logs/ Clustering analysis logs├── Hexane/ 5,160 peptides│ ├── Trajectories/ *.pdb (100 frames per peptide)│ ├── Structures/ Representative conformations from clustering│ └── Logs/ Clustering analysis logs├── CHCl3/ 6 peptides└── CycPeptMPDB-4D.csv metadata & molecular descriptors Data File and Column Descriptions The main metadata file, CycPeptMPDB-4D.csv, provides experimental permeability values (PAMPA) alongside physics-based descriptors derived from the MD trajectories. Column Description CycPeptMPDB_ID Unique identifier from the original CycPeptMPDB, inherited from CycPeptMPDB Source Reference literature for the peptide data, inherited from CycPeptMPDB SMILES Simplified Molecular Input Line Entry System, inherited from CycPeptMPDB Sequence Peptide sequence, inherited from CycPeptMPDB Original_Name_in_Source_Literature Original peptide designation in the source literature, inherited from CycPeptMPDB Structurally_Unique_ID Identifier grouping structurally identical peptides across sources, inherited from CycPeptMPDB PAMPA Experimental membrane permeability (log cm/s), mesured by PAMPA, inherited from CycPeptMPDB Monomer_Length Total number of amino residues in the peptide Monomer_Length_in_Main_Chain Number of amino residues in the main-chain cycle (differs from Monomer_Length for lariat-shaped peptides) Molecule_Shape Structural topology (Circle or Lariat) Water_avgRMSD_All Average RMSD of all heavy atoms in water simulation (A) Water_avgRMSD_BackBone Average RMSD of backbone heavy atoms in water (A) Water_argRG Mean radius of gyration across the trajectory Water_Desolvation_Free_Energy Computed desolvation free energy via MMPBSA (kcal/mol) Water_3D_SASA Solvent Accessible Surface Area in water (A²) Water_3D_NPSA Non-Polar Surface Area in water (A²) Water_3D_PSA Polar Surface Area in water (A²) Water_RepFrame Frame index of the center frame of the largest cluster in water trajectory Hexane_avgRMSD_All Average RMSD of all heavy atoms in hexane simulation (A) Hexane_avgRMSD_BackBone Average RMSD of backbone heavy atoms in hexane (A) Hexane_argRG Mean radius of gyration across the trajectory Hexane_3D_SASA Solvent Accessible Surface Area in hexane (A²) Hexane_3D_NPSA Non-Polar Surface Area in hexane (A²) Hexane_3D_PSA Polar Surface Area in hexane (A²) Hexane_RepFrame Frame index of the center frame of the largest cluster in hexane trajectory