dataset · Zenodo (CERN European Organization for Nuclear Research)
This dataset provides molecular dynamics trajectory and simulation data evaluating de novo-designed macrocyclic peptide binders targeting Staphylococcus aureus Sortase A. The repository encompasses three distinct peptide complexes, designated SMP01, SMP41, and SMP103. Each complex was evaluated using three independent, two-microsecond all-atom simulations, yielding six microseconds of production sampling per complex and eighteen microseconds of total sampling. The deposited files include processed protein-only trajectories sampled at one-hundred-picosecond intervals, production run-input parameters, final coordinate structures, and energy records. Solvent and ions were removed from the trajectories to reduce storage requirements while preserving the full two-microsecond duration. Associated public repositories supply the coordinate files, parameters, analysis scripts, and molecular topologies that explicitly encode the head-to-tail covalent cyclisation of the peptides.
Staphylococcus aureus is a major bacterial pathogen, and Sortase A is an established target for therapeutic intervention. By releasing open simulation trajectories and code for newly designed macrocyclic peptide binders, this resource allows independent researchers to inspect, reproduce, and analyse the physical stability and binding behaviours of candidate molecules at atomic resolution.
This work represents early-stage computational drug discovery research. The dataset could be utilised by academic or pharmaceutical computational biophysicists seeking to develop or refine macrocyclic peptide candidates targeting bacterial Sortase A. As the abstract describes purely in silico simulation trajectories and structural models, physical synthesis, in vitro binding validation, and subsequent biological testing would be required before any commercial application pathway could emerge.
AI-generated from the published abstract. Always read the original work before citing.
This dataset accompanies the computational study of de novo-designed macrocyclic peptide binder candidates targeting Staphylococcus aureus Sortase A (SrtA). It contains molecular dynamics trajectory and simulation data for three SrtA-macrocyclic peptide complexes: SMP01-SrtA, SMP41-SrtA, and SMP103-SrtA. For each complex, three independent 2-μs all-atom molecular dynamics simulations (Replicas 1-3) are deposited, corresponding to a total production sampling time of 6 μs per peptide–SrtA complex and 18 μs across the three designed complexes. For each replica, the following files are provided: .xtc – processed protein-only trajectory containing Sortase A and the corresponding macrocyclic peptide, spanning the complete 2-μs production simulation and sampled at 100-ps intervals. .tpr – original GROMACS production run-input file for the corresponding explicitly solvated simulation. .edr – original GROMACS energy file for the corresponding production simulation. .gro – final coordinate structure of the complete explicitly solvated system from the corresponding production simulation. Trajectory size reduction The original production trajectories contain the complete explicitly solvated systems, including Sortase A, the macrocyclic peptide, water molecules, and ions, and were written at a substantially higher temporal frequency. These full-resolution trajectories are large (approximately 20 GB or more per 2-μs simulation). To enable practical public deposition while preserving the complete temporal extent of every simulation, the deposited .xtc trajectories were generated from the original production trajectories using GROMACS. Two reductions were applied: Solvent and ions were omitted from the deposited XTC files, retaining Sortase A and the corresponding macrocyclic peptide; and The trajectories were temporally downsampled to 100-ps intervals. No truncation of the production simulations was performed. Each deposited XTC therefore spans the complete 2 μs of its corresponding replica. A 2-μs trajectory sampled at 100-ps intervals contains 20,001 coordinate frames, spanning 0 to 2,000 ns. The original full-system, full-resolution production trajectories were used for the molecular dynamics analyses reported in the associated manuscript. The processed trajectories deposited here are provided to facilitate public access, structural inspection, independent trajectory analysis, and verification of the reported simulation behavior while avoiding unnecessary storage of high-frequency solvent coordinates. The accompanying .tpr and .edr files correspond to the original explicitly solvated production systems and are retained to provide simulation provenance and access to the original production parameters and energetic information. Associated simulation inputs and analysis scripts The small, human-readable files required to inspect and reproduce the molecular dynamics setup—including starting coordinates (.pdb and .gro), GROMACS molecular topologies (.top and .itp), position-restraint files, simulation parameter files (.mdp), and the CHARMM36 force-field distribution used for system preparation and simulation, are publicly available in the associated GitHub repository: Molecular dynamics input files:https://github.com/Olanrewaju-Durojaye/Molecular-Dynamics-Input-Files-for-De-Novo-Macrocyclic-Peptide-Sortase-A-Complexes The deposited topology files explicitly encode the head-to-tail covalent cyclization of SMP01, SMP41, and SMP103, allowing independent verification that the peptides were simulated as macrocyclic rather than linear structures. Custom scripts used for structural, cross-predictor, molecular dynamics, contact-occupancy, and enhanced-sampling analyses are available separately at: Analysis scripts:https://github.com/Olanrewaju-Durojaye/Scripts_for_SMP_Project_analyses Dataset composition The Zenodo dataset contains: SrtA-SMP01 complex: three independent 2-μs production replicas SrtA-SMP41 complex: three independent 2-μs production replicas SrtA-SMP103 complex: three independent 2-μs production replicas This corresponds to nine independent production trajectories and 18 μs of aggregate production MD sampling across the three designed peptide–SrtA complexes. Simulation software: GROMACS 2026.0-dev-20250915-1e492c61b4Force field: CHARMM36 (charmm36-jul2021.ff)Water model: TIP3P Full methodological details, simulation conditions, trajectory analyses, and statistical comparisons are provided in the associated manuscript.
This page summarises published work. The authoritative version sits with the publisher.
DOI: 10.5281/zenodo.21888185
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