# JCIM Application Note Submission TODO
This document tracks the required changes to submit PDBRust to the [Journal of Chemical Information and Modeling (JCIM)](https://pubs.acs.org/journal/jcisd8) as an Application Note.
## JCIM Application Note Requirements
**Word Limit**: ~3000-4000 words (current paper fits within this range)
**Format**: ACS LaTeX template or Word
**Article Type**: Application Note (software/tool description)
## Paper Format Conversion
### Template & Formatting
- [ ] Download ACS LaTeX template from [ACS Author Guidelines](https://publish.acs.org/publish/author_guidelines?coden=jcisd8)
- [ ] Convert `pdbrust_paper.tex` to ACS format using `achemso` package
- [ ] Add `\documentclass[journal=jcisd8,manuscript=article]{achemso}`
- [ ] Update bibliography style to ACS format (`achemso` or `acschemguide`)
### Required Metadata
- [ ] Add corresponding author designation with email
- [ ] Add ORCID for all authors
- [ ] Add keywords (5-7 keywords recommended)
- [ ] Add abbreviations section if needed
### Graphical Abstract / TOC Graphic
- [ ] Create TOC graphic (required for all JCIM submissions)
- Size: 3.25 × 1.75 inches (8.25 × 4.45 cm)
- Resolution: 300 dpi minimum
- Should visually summarize the software/workflow
- Current TikZ figure could be adapted
## Required Sections for Application Note
### 1. Abstract (existing - adapt)
- [ ] Keep under 150 words
- [ ] Summarize key functionality and performance claims
- [ ] Mention availability
### 2. Introduction (existing - review)
- [ ] Clearly state the problem being addressed
- [ ] Brief overview of existing solutions and their limitations
- [ ] Introduce the solution (PDBRust)
### 3. Methods / Implementation (expand current "Features")
- [ ] Describe software architecture
- [ ] Explain key design decisions (why Rust, feature flags, etc.)
- [ ] Document dependencies and system requirements
- [ ] Describe Python bindings if targeting Python users
### 4. Results / Validation (existing - expand)
- [ ] Performance benchmarks (already included)
- [ ] Full PDB archive validation (already included)
- [ ] Add example workflow/use case demonstration
- [ ] Consider adding comparison with more tools (Gemmi, BioJulia)
### 5. Discussion / Use Cases (existing - can keep brief)
- [ ] Target applications
- [ ] Limitations and future work
- [ ] Integration with existing pipelines
### 6. Availability and Implementation
- [ ] Software availability statement
- [ ] License information (MIT)
- [ ] Repository URL
- [ ] Package manager installation (crates.io, PyPI)
- [ ] Documentation URL
- [ ] Version number of software described
### 7. Associated Content (Supporting Information)
- [ ] Consider adding SI with:
- Extended API documentation
- Additional benchmarks
- Installation troubleshooting
- More code examples
## References Requirements
- [ ] Use ACS citation style (superscript numbers or author-date)
- [ ] Ensure all software tools cited have proper references
- [ ] Add DOI for all references where available
- [ ] Cite key related work:
- Biopython
- MDAnalysis
- Gemmi
- PDB/RCSB
## Repository Requirements
### Already Complete
- [x] Open source license (MIT)
- [x] Public repository (GitHub)
- [x] Issue tracker (GitHub Issues)
- [x] Documentation (docs.rs)
- [x] Tests (cargo test)
- [x] Package manager distribution (crates.io, PyPI)
- [x] DOI for citation (Zenodo: 10.5281/zenodo.18232203)
### Recommended Additions
- [ ] Create `CONTRIBUTING.md` with:
- How to report bugs
- How to submit pull requests
- Development setup instructions
- Code style guidelines
- [ ] Create `CODE_OF_CONDUCT.md`
- Use [Contributor Covenant](https://www.contributor-covenant.org/)
## Figures and Tables
### Current Figures
- [x] Figure 1: Architecture diagram (TikZ) - may need reformatting for ACS
### Current Tables
- [x] Table 1: Performance benchmarks
- [x] Table 2: Full PDB validation results
### Consider Adding
- [ ] Table comparing features with other libraries (Biopython, MDAnalysis, Gemmi)
- [ ] Figure showing example workflow or code snippet
## ACS-Specific Requirements
### Data Availability Statement
- [ ] Add statement about data availability (benchmark data, test files)
### FAIR Data Principles
- [ ] Ensure software meets FAIR principles (Findable, Accessible, Interoperable, Reusable)
- [ ] Include permanent identifier (Zenodo DOI)
### Code Availability
- [ ] Provide GitHub URL
- [ ] Specify version/commit hash for reproducibility
- [ ] Consider archiving specific version on Zenodo
## Submission Checklist
Before submitting via [ACS Paragon Plus](https://acsparagonplus.acs.org/):
### Manuscript
- [ ] Manuscript in ACS format (LaTeX or Word)
- [ ] All figures embedded or as separate high-resolution files
- [ ] TOC graphic prepared (separate file)
- [ ] Supporting Information prepared (if applicable)
### Cover Letter
- [ ] Write cover letter explaining:
- Novelty and significance of the software
- Why JCIM is appropriate venue
- Potential reviewer suggestions (optional)
### Author Information
- [ ] All author names, affiliations, ORCIDs confirmed
- [ ] Corresponding author designated
- [ ] Author contributions statement (CRediT taxonomy)
### Declarations
- [ ] Conflict of interest statement
- [ ] Funding information
- [ ] AI usage disclosure (if applicable)
### Software
- [ ] Software is publicly available
- [ ] Documentation is complete
- [ ] All tests passing
- [ ] Version to be described in paper is tagged/released
## Timeline Estimate
| Convert to ACS format | Not started |
| Create TOC graphic | Not started |
| Expand Methods section | Not started |
| Update references to ACS style | Not started |
| Add comparison table | Not started |
| Create CONTRIBUTING.md | Not started |
| Create CODE_OF_CONDUCT.md | Not started |
| Write cover letter | Not started |
| Final proofreading | Not started |
| Submit | Not started |
## References
- JCIM Author Guidelines: https://publish.acs.org/publish/author_guidelines?coden=jcisd8
- ACS LaTeX Template: https://www.acs.org/content/acs/en/pubs/latex-templates.html
- JCIM Application Notes examples: Search recent JCIM issues for "Application Note"
- ACS Paragon Plus (submission): https://acsparagonplus.acs.org/
## Notes
- JCIM is a peer-reviewed journal with higher impact than JOSS
- Application Notes are appropriate for software tools
- Expect 2-3 reviewers with expertise in cheminformatics/structural biology
- Review process typically takes 4-8 weeks
- Open Access option available (ACS AuthorChoice)