[PRE REVIEW]: TinkerModellor: An Efficient Tool for Building Biological Systems in Tinker Simulations

[editorialbot]

Submitting author: @Hsuchein (Xujian Wang)
Repository: https://github.com/WanluLigroupUCSD/TinkerModellor
Branch with paper.md (empty if default branch): joss
Version: v1.0
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (659.8 files/s, 50375.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          14            191            208            533
XML                              1              0              0            307
Markdown                         3             69              0            153
TeX                              1             18              0            153
YAML                             3              1              4             99
make                             1              4              4             12
-------------------------------------------------------------------------------
SUM:                            23            283            216           1257
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1243

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1016/j.softx.2015.06.001 may be a valid DOI for title: GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
- 10.1021/jacs.6b12265.s001 may be a valid DOI for title: The Importance of the Scaffold for de Novo Enzymes: A Case Study with Kemp Eliminase
- 10.26434/chemrxiv.13615853 may be a valid DOI for title: Local Electric Fields as a Natural Switch of Heme-Iron Protein Reactivity
- 10.1039/d3sc02982d may be a valid DOI for title: From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics
- 10.3390/antib7030023 may be a valid DOI for title: OptMAVEn-2.0: De novo Design of Variable Antibody Regions against Targeted Antigen Epitopes
- 10.1016/b978-0-12-821978-2.00018-0 may be a valid DOI for title: Electric Fields and Enzyme Catalysis
- 10.1021/acscentsci.0c01556 may be a valid DOI for title: Catalytic Principles from Natural Enzymes and Translational Design Strategies for Synthetic Catalysts
- 10.21105/joss.02576 may be a valid DOI for title: ELECTRIC: Electric fields Leveraged from multipole Expansion Calculations in Tinker Rapid Interface Code
- 10.1021/ct200304d may be a valid DOI for title: Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules
- 10.1021/acs.jcim.2c01048.s001 may be a valid DOI for title: Characterizing Ion-Polymer Interactions in Aqueous Environment with Electric Fields
- 10.1088/2516-1075/ac509f may be a valid DOI for title: Beyond structural analysis of molecular enzyme-inhibitor interactions
- 10.1021/acs.jctc.7b01169.s001 may be a valid DOI for title: AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids
- 10.1021/acs.jpcb.2c00765.s001 may be a valid DOI for title: Tuning the Catalytic Activity of Synthetic Enzyme KE15 with DNA
- 10.1016/0263-7855(96)00018-5 may be a valid DOI for title: VMD: Visual Molecular Dynamics
- 10.1021/acs.jctc.0c01286.s001 may be a valid DOI for title: Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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[Kevin-Mattheus-Moerman]

@Hsuchein thanks for this submission. I am the AEiC for this track. I have just checked your repository, and reviewed the above software report (stating number of lines of code etc.). Unfortunately this work is not in scope for JOSS as it stands as it does not conform to our substantial scholarly effort criteria.

We will now proceed to reject this submission.

We hope you will consider JOSS for any future (re)submissions that are of a more substantial nature.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.