A combined in silico approach to design peptide ligands with increased receptor-subtype selectivity

This Dataset has a corresponding publication:

"A combined in silico approach to design peptide ligands with increased receptor-subtype selectivity" ~ Adam Zech, Victoria Most, Anna Mutti, Passainte Ibrahim, Regine Heilbronn, Christoph Schwarzer, Peter W. Hildebrand, René Staritzbichler

Doi: 10.1016/j.jmb.2025.169006

The dataset has the results of the pipeline described in the paper:

• md_simulations

includes approximately 7.5 microseconds of simulations in .xtc trajectories for DAMGO-(MOPr/KOPr/DOPr)-GiaCT complexes with their respective .pdb files for analysis. The .pdb files are the first frame of each of the simulations. Each simulation is the concatenation of three separate runs of approximately 2.5 microseconds of simulation. 

• final_files 

has the files which are created by the script analyze_refinement.py. The file all_seq_scores.txt (corresponding to Table 1 of the paper) is a concatenation of the other seq*.txt files, while main_seq_scores.txt (corresponding to Fig. 4 of the paper) is a reduction of the files found in all_seq_scores.txt.

• analyze_refinement.py

is the script which takes respective rescored_flexpepdock.txt and seq_pdb_score.txt files from corresponding kappa and mu mutations and creates the files found in final_files.

• kappa_from_G3A/mu_from_G3A

has all the final design files starting from a DynB G3A mutant in the respective receptors. There are two directories (refinement and refinement_2) containing the .pdb structures of the design and there are the respective rescored_flexpepdock.txt/rescored_flexpepdock_2.txt and seq_pdb_score.txt/seq_pdb_score_2.txt files scoring these designs.

• kappa_from_WT/mu_from_WT:

has all the final design files starting from a DynB WT in the respective receptors. There is one directory (relaxed) containing the .pdb structures of the design and there are the respective rescored_flexpepdock.txt and seq_pdb_score.txt files scoring these designs.