[PRE REVIEW]: Af2-analysis: a Python package for Alphafold 2 analysis

[editorialbot]

Submitting author: !--author-handle-->@samuelmurail<!--end-author-handle-- (Samuel Murail) Repository: https://github.com/samuelmurail/af2_analysis Branch with paper.md (empty if default branch): Version: v0.0.2 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.20 s (502.3 files/s, 49574.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21            739            770           2257
JSON                            53              0              0            774
HTML                             1              4              1            443
XML                              1              0              0            342
Markdown                         5            111              0            325
reStructuredText                 7            184            206            155
Jupyter Notebook                 2              0           2941            126
TeX                              1              9              0            114
Bourne Shell                     1              8              2             85
make                             2             22              7             69
TOML                             2              9              1             64
YAML                             2              9             13             43
DOS Batch                        1              8              1             26
CSV                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                           100           1103           3942           4825
-------------------------------------------------------------------------------

Commit count by author:

   107  samuelmurail
    15  Samuel Murail
     1  Alaa REGUEI
     1  regueiala

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1038/s41586-021-03819-2 is OK
- 10.1101/2021.10.04.463034 is OK
- 10.1093/bioinformatics/btad573 is OK
- 10.1093/bioinformatics/btad424 is OK
- 10.1101/2024.02.19.580970 is OK
- 10.1101/2024.02.19.580970 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- 10.1101/2021.08.15.456425 may be a valid DOI for title: ColabFold: making protein folding accessible to al...
- 10.1371/journal.pone.0161879 may be a valid DOI for title: DockQ: a quality measure for protein-protein docki...
- 10.1038/s41467-022-28865-w may be a valid DOI for title: Improved prediction of protein-protein interaction...

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 465

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v2.0 (Check here for OSI approval)

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

Project RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugates Submitting author: @moritzobenauer Handling editor: @jromanowska (Active) Reviewers: @taoliu032, @lorenzo-rovigatti Similarity score: 0.7172

SolvationAnalysis: A Python toolkit for understanding liquid solvation structure in classical molecular dynamics simulations Submitting author: @orionarcher Handling editor: @zhubonan (Active) Reviewers: @amritagos, @arose Similarity score: 0.7043

MembraneAnalysis.jl: A Julia package for analyzing molecular dynamics simulations of lipid membranes Submitting author: @amiralih Handling editor: @majensen (Active) Reviewers: @tonigi, @davidnsousa Similarity score: 0.6937

dfba: Software for efficient simulation of dynamic flux-balance analysis models in Python Submitting author: @davidtourigny Handling editor: @marcosvital (Active) Reviewers: @jdbrunner, @pstjohn, @synchon Similarity score: 0.6916

DeepOF: a Python package for supervised and unsupervised pattern recognition in mice motion tracking data Submitting author: @lucasmiranda42 Handling editor: @emdupre (Active) Reviewers: @cellistigs, @edeno Similarity score: 0.6914

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[samuelmurail]

@editorialbot commands

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Hello @samuelmurail, here are the things you can ask me to do:

# List all available commands
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# Get a list of all editors's GitHub handles
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# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
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@editorialbot check repository

# Check the references of the paper for missing DOIs
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@editorialbot generate preprint

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[samuelmurail]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

dms2dfe: Comprehensive Workflow for Analysis of Deep Mutational Scanning Data Submitting author: @rraadd88 Handling editor: @tracykteal (Retired) Reviewers: @afrubin Similarity score: 0.7176

SolvationAnalysis: A Python toolkit for understanding liquid solvation structure in classical molecular dynamics simulations Submitting author: @orionarcher Handling editor: @zhubonan (Active) Reviewers: @amritagos, @arose Similarity score: 0.7024

MembraneAnalysis.jl: A Julia package for analyzing molecular dynamics simulations of lipid membranes Submitting author: @amiralih Handling editor: @majensen (Active) Reviewers: @tonigi, @davidnsousa Similarity score: 0.6898

DeepOF: a Python package for supervised and unsupervised pattern recognition in mice motion tracking data Submitting author: @lucasmiranda42 Handling editor: @emdupre (Active) Reviewers: @cellistigs, @edeno Similarity score: 0.6891

dfba: Software for efficient simulation of dynamic flux-balance analysis models in Python Submitting author: @davidtourigny Handling editor: @marcosvital (Active) Reviewers: @jdbrunner, @pstjohn, @synchon Similarity score: 0.6882

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[samuelmurail]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1038/s41586-021-03819-2 is OK
- 10.1038/s41592-022-01488-1 is OK
- 10.1101/2021.10.04.463034 is OK
- 10.1093/bioinformatics/btad573 is OK
- 10.1093/bioinformatics/btad424 is OK
- 10.1101/2024.02.19.580970 is OK
- 10.1371/journal.pone.0161879 is OK
- 10.1101/2024.02.19.580970 is OK
- 10.1038/s41467-022-28865-w is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[samuelmurail]

Here is a list of potential reviewers, which should have some knowledge about protein/DNA/RNA structure and Alphafold.

• rvhonorato
• HubLot
• George Anthony Pantelo...
• Michael Montgomery Henry
• joaorodrigues
• arose
• Priyanshu R Gupta
• Anshuman Kumar

[samuelmurail]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.20 s (496.5 files/s, 52204.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21            727            770           2900
JSON                            53              0              0            774
HTML                             1              4              1            443
XML                              1              0              0            344
Markdown                         5            111              0            324
reStructuredText                 7            184            206            155
Jupyter Notebook                 2              0           2941            126
TeX                              1              9              0            117
Bourne Shell                     1              8              2             85
TOML                             2             11              1             72
make                             2             22              7             68
YAML                             2              9             13             43
DOS Batch                        1              8              1             26
CSV                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                           100           1093           3942           5479
-------------------------------------------------------------------------------

Commit count by author:

   114  samuelmurail
    15  Samuel Murail
     1  Alaa REGUEI
     1  regueiala

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 465

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v2.0 (Check here for OSI approval)