https://github.com/batoolmm/evi1-dnmt3
Molecular dynamics study for the interaction between EVI1-DNMT3
Science Score: 33.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: acs.org -
✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
○Institutional organization owner
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○Scientific vocabulary similarity
Low similarity (4.3%) to scientific vocabulary
Repository
Molecular dynamics study for the interaction between EVI1-DNMT3
Basic Info
- Host: GitHub
- Owner: BatoolMM
- Language: PostScript
- Default Branch: main
- Size: 47.6 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
EVI1-DNMT3
Molecular dynamics study for the interaction between EVI1-DNMT3
Creating the DNMT3 Structure
We used AlphaFold for accuracy > 70
Extracted residues 474-912
select st, b > 70
select st, i. 474-912
Saved it and manipulated in PyMOL as PDBx/mmCIF
Write connect reords for all bonds
Retain segment identifier and atoms ids
Write HEADER for every object
Force Field
We used CHARMM36 force field and changed all the setting in the .mdp files to mach the CHARMM36 settings.
constraints = h-bonds
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
DispCorr = no
Added SEP in residuetype.dat and changed CAL to CL in ions.itp
The advantages of CHARMM36 force field is that it was recently optimised to include functional groups such as phosphorylation. Other force fields can be modified as here and here.
Owner
- Name: Batool Almarzouq
- Login: BatoolMM
- Kind: user
- Company: University of Liverpool, Alan Turing Institute
- Website: https://batool-almarzouq.netlify.app/
- Twitter: batool664
- Repositories: 48
- Profile: https://github.com/BatoolMM
Ph.D. in Biochemistry. Experience in cancer bioinformatics, RNA-Seq, network biology, pathway enrichment, and integrated –omics analyses, Docker, HPC (She/her).
GitHub Events
Total
Last Year
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| BatoolMM | b****l@l****k | 28 |
| Batool | m@M****l | 6 |
| Batool Almarzouq | b****l@l****k | 4 |
| Batool Almarzouq | b****l@v****k | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0