https://github.com/m3g/complexmixtures.jl
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
Science Score: 49.0%
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Repository
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
Basic Info
- Host: GitHub
- Owner: m3g
- License: mit
- Language: Julia
- Default Branch: main
- Homepage: https://m3g.github.io/ComplexMixtures.jl/
- Size: 60.9 MB
Statistics
- Stars: 20
- Watchers: 2
- Forks: 3
- Open Issues: 1
- Releases: 0
Topics
Metadata Files
README.md
ComplexMixtures.jl
A package to study the structure of solutions formed by solutes and solvents of complex molecular shapes.
Documentation:
The documentation is available at: https://m3g.github.io/ComplexMixtures.jl
Examples
A series of examples of applications can be found at: https://m3g.github.io/ComplexMixtures.jl/stable/examples
Overview
ComplexMixtures is a package to study the solute and solvent interactions of mixtures of molecules of complex shape. Conventional radial distribution functions are not appropriate to represent the structure of a solvent around a solute with many atoms, and a variable, non-spherical shape.
Typical solutes of complex shape are proteins, nucleic acids, and polymers in general. Smaller molecules like lipids, carbohydrates, etc, are also complex enough such that representing the structure of the solution of those molecules with distribution functions is not trivial.
Minimum-Distance Distribution Functions (MDDFs) are a very general and practical way to represent solute-solvent interactions for molecules with arbitrarily complex sizes and geometries. Briefly, instead of computing the density distribution function of a particular atom or the center-of-mass of the molecules, one computes the distribution function of the minimum-distance between any solute and solvent atoms. This provides a size and shape-independent distribution which is very natural to interpret in terms of molecular interactions.
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Minimum-distance distribution function and its decomposition into molecular groups. |
Additionally, the MDDFs can be decomposed into contributions of each type of atom (or groups of atoms) of the solute and solvent molecules, such that the profiles of the distributions can be interpreted in terms of the chemical nature of the species involved in the interactions at each distance.
Finally, as with radial distribution functions, MDDFs can be used to compute Kirkwood-Buff integrals to connect the accumulation or depletion of the solvents components to thermodynamic properties, like protein structural stability, solubility, and others.
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Density map of a solvent in the vicinity of each protein residue. |
References
If this package was useful to you, please cite the following articles:
L. Martínez, ComplexMixtures.jl: Investigating the structure of solutions of complex-shaped molecules from a solvent-shell perspective. J. Mol. Liq. 347, 117945, 2022. [Full Text]
L. Martínez, S. Shimizu, Molecular interpretation of preferential interactions in protein solvation: a solvent-shell perspective by means of minimum-distance distribution functions. J. Chem. Theor. Comp. 13, 6358–6372, 2017. [Full Text]
Additional resources
Please go to http://m3g.iqm.unicamp.br to find additional resources and publications associated with this project.
Owner
- Name: Martínez Molecular Modeling Group
- Login: m3g
- Kind: user
- Location: Campinas, SP, Brazil
- Company: Institute of Chemistry - University of Campinas (UNICAMP) - Brazil
- Website: http://m3g.iqm.unicamp.br
- Repositories: 20
- Profile: https://github.com/m3g
GitHub Events
Total
- Create event: 77
- Commit comment event: 52
- Issues event: 5
- Release event: 24
- Watch event: 4
- Delete event: 57
- Issue comment event: 56
- Push event: 296
- Pull request event: 92
- Fork event: 3
Last Year
- Create event: 77
- Commit comment event: 52
- Issues event: 5
- Release event: 24
- Watch event: 4
- Delete event: 57
- Issue comment event: 56
- Push event: 296
- Pull request event: 92
- Fork event: 3
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 742
- Total Committers: 7
- Avg Commits per committer: 106.0
- Development Distribution Score (DDS): 0.239
Top Committers
| Name | Commits | |
|---|---|---|
| Leandro Martinez | l****o@i****r | 565 |
| Leandro Martinez | l****e@u****r | 156 |
| Martínez Molecular Modeling Group | l****8@g****m | 7 |
| Leandro Martínez | 3****q@u****m | 6 |
| github-actions[bot] | 4****]@u****m | 3 |
| Leandro Martínez | 3****8@u****m | 3 |
| Chris de Graaf | me@c****v | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 9
- Total pull requests: 105
- Average time to close issues: about 1 month
- Average time to close pull requests: 3 days
- Total issue authors: 6
- Total pull request authors: 4
- Average comments per issue: 15.67
- Average comments per pull request: 0.52
- Merged pull requests: 82
- Bot issues: 0
- Bot pull requests: 5
Past Year
- Issues: 3
- Pull requests: 74
- Average time to close issues: 15 days
- Average time to close pull requests: about 19 hours
- Issue authors: 3
- Pull request authors: 2
- Average comments per issue: 0.33
- Average comments per pull request: 0.61
- Merged pull requests: 63
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lmiq (4)
- mbrosz (1)
- koreyr (1)
- SnehaSahuvs4 (1)
- omidshy (1)
- JuliaTagBot (1)
Pull Request Authors
- lmiq (135)
- github-actions[bot] (3)
- inkydragon (2)
- dependabot[bot] (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- julia 14 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 152
juliahub.com: ComplexMixtures
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
- Homepage: https://m3g.github.io/ComplexMixtures.jl/
- Documentation: https://docs.juliahub.com/General/ComplexMixtures/stable/
- License: MIT
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Latest release: 2.14.4
published 8 months ago
Rankings
Dependencies
- JuliaRegistries/TagBot v1 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- codecov/codecov-action v3 composite
- julia-actions/julia-buildpkg latest composite
- julia-actions/julia-processcoverage v1 composite
- julia-actions/julia-runtest latest composite
- julia-actions/setup-julia v1 composite