2025_PTM_colocalization.io

Supplementary data

A study of co-localization of post-translational modifications of human histones: genome annotation analysis and modeling the effect of multiple modifications on nucleosome structure

GitHub repository

https://github.com/intbio/2025_PTM_colocalization.io

Interactive preview of MD trajectories

• N_canon - Canonical nucleosome with full tails (PDB ID 1KX5), run_1
• N₁^run_1 - Nucleosome 1KX5 with modifications H3K14ac and H3K23ac, run_1
• N₁^run_2 - Nucleosome 1KX5 with modifications H3K14ac and H3K23ac, run_2
• N₂^run_1 - Nucleosome 1KX5 with modifications H4K5ac, H3K9ac, H3K27ac, H3K56ac, run_1
• N₂^run_2 - Nucleosome 1KX5 with modifications H4K5ac, H3K9ac, H3K27ac, H3K56ac, run_2
• N₃^run_1 - Nucleosome 1KX5 with modifications H4K5ac, H3K9ac, H3K27ac, H3K56ac + H3K18ac, H4K91ac, H2BK5ac, H4K8ac, run_1
• N₃^run_2 - Nucleosome 1KX5 with modifications H4K5ac, H3K9ac, H3K27ac, H3K56ac + H3K18ac, H4K91ac, H2BK5ac, H4K8ac, run_2
• N₄^run_1 - Nucleosome 1KX5 with modifications H3K18ac, H3K4ac, H4K91ac, H4K8ac, H2AK5ac, H2BK5ac, H2BK12ac, H2BK20ac, H2BK15ac, H2BK120ac, run_1
• N₄^run_2 - Nucleosome 1KX5 with modifications H3K18ac, H3K4ac, H4K91ac, H4K8ac, H2AK5ac, H2BK5ac, H2BK12ac, H2BK20ac, H2BK15ac, H2BK120ac, run_2
• N₅^run_1 - Nucleosome 1KX5 with all presented acetylations, run_1

Trajectory files

• N_canon - Canonical nucleosome with full tails (PDB ID 1KX5), run_1: pdb, xtc
• N₁^run_1 - Nucleosome 1KX5 with modifications H3K14ac and H3K23ac, run_1: pdb, xtc
• N₁^run_2 - Nucleosome 1KX5 with modifications H3K14ac and H3K23ac, run_2: pdb, xtc
• N₂^run_1 - Nucleosome 1KX5 with modifications H4K5ac, H3K9ac, H3K27ac, H3K56ac, run_1: pdb, xtc
• N₂^run_2 - Nucleosome 1KX5 with modifications H4K5ac, H3K9ac, H3K27ac, H3K56ac, run_2: pdb, xtc
• N₃^run_1 - Nucleosome 1KX5 with modifications H4K5ac, H3K9ac, H3K27ac, H3K56ac + H3K18ac, H4K91ac, H2BK5ac, H4K8ac, run_1: pdb, xtc
• N₃^run_2 - Nucleosome 1KX5 with modifications H4K5ac, H3K9ac, H3K27ac, H3K56ac + H3K18ac, H4K91ac, H2BK5ac, H4K8ac, run_2: pdb, xtc
• N₄^run_1 - Nucleosome 1KX5 with modifications H3K18ac, H3K4ac, H4K91ac, H4K8ac, H2AK5ac, H2BK5ac, H2BK12ac, H2BK20ac, H2BK15ac, H2BK120ac, run_1: pdb, xtc
• N₄^run_2 - Nucleosome 1KX5 with modifications H3K18ac, H3K4ac, H4K91ac, H4K8ac, H2AK5ac, H2BK5ac, H2BK12ac, H2BK20ac, H2BK15ac, H2BK120ac, run_2: pdb, xtc
• N₅^run_1 - Nucleosome 1KX5 with all presented acetylations, run_1: pdb, xtc

Force field

https://github.com/intbio/gromacs_ff/amber19sb_parmbsc1_opc.ff