bamboo
Protein Secondary Structure Prediction Using the Bamboo Method
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.9%) to scientific vocabulary
Last synced: 11 months ago
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Repository
Protein Secondary Structure Prediction Using the Bamboo Method
Basic Info
- Host: GitHub
- Owner: dbdahl
- Language: Scala
- Default Branch: master
- Size: 20.8 MB
Statistics
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Created about 9 years ago
· Last pushed almost 3 years ago
https://github.com/dbdahl/bamboo/blob/master/
# bamboo: Protein Secondary Structure Prediction Using the Bamboo Method
Determining the primary structure (i.e., amino acid sequence) of a protein has become cheaper, faster, and more accurate. Higher order protein structure provides insight into a proteins function in the cell. Understanding a proteins secondary structure is a first step towards this goal. Therefore, a number of computational prediction methods have been developed to predict secondary structure from just the primary amino acid sequence. The most successful methods use machine learning approaches that are quite accurate, but do not directly incorporate structural information. As a step towards improving secondary structure reduction given the primary structure, we propose a Bayesian model based on the knob-socket model of protein packing in secondary structure. The method considers the packing influence of residues on the secondary structure determination, including those packed close in space but distant in sequence. By performing an assessment of our method on 2 test sets we show how incorporation of multiple sequence alignment data, similarly to PSIPRED, provides balance and improves the accuracy of the predictions. Software implementing the methods is provided as a web application and a stand-alone implementation
## Installation
In R, install the package by executing:
```R
install.packages("remotes")
remotes::install_github("dbdahl/rscala/R/rscala")
remotes::install_github("dbdahl/bamboo/R/bamboo")
```
## Resources
* [Paper](https://doi.org/10.1371/journal.pone.0109832) describes the methods implemented in this package.
```R
library(bamboo)
example(bamboo)
help(bamboo)
```
Owner
- Name: David B. Dahl
- Login: dbdahl
- Kind: user
- Location: United States
- Company: Brigham Young University
- Website: https://dahl.byu.edu
- Repositories: 10
- Profile: https://github.com/dbdahl
GitHub Events
Total
Last Year
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| David B. Dahl | d****l@s****u | 27 |
| David B. Dahl | d****d@d****g | 16 |
| David B. Dahl | d****l | 1 |
Committer Domains (Top 20 + Academic)
ddahl.org: 1
stat.byu.edu: 1
Packages
- Total packages: 1
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Total downloads:
- cran 239 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 8
- Total maintainers: 1
cran.r-project.org: bamboo
Protein Secondary Structure Prediction Using the Bamboo Method
- Homepage: https://github.com/dbdahl/bamboo
- Documentation: http://cran.r-project.org/web/packages/bamboo/bamboo.pdf
- License: GPL-3
- Status: removed
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Latest release: 0.9.25
published over 6 years ago
Rankings
Stargazers count: 28.5%
Forks count: 28.8%
Dependent packages count: 29.8%
Average: 31.9%
Dependent repos count: 35.5%
Downloads: 37.0%
Maintainers (1)
Last synced:
almost 3 years ago
Dependencies
R/bamboo/DESCRIPTION
cran
- R >= 3.5.0 depends
- rscala >= 3.2.18 imports