Data for the internship at the MPI
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下载链接：
https://zenodo.org/record/11942464
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资源简介：
Data for the internship at the MPI
Repositories
Code
protein-structure-analysis -- A snakemake pipeline that allows for comparison of protein complexes using the USalign algorithm, invesitgation of ligands using PLIP, plotting of a ramachandran profile, enumerating steric clashes, analysis of surface accessibility and plotting of the beta-factor column.
snakemake-template -- Tempate for snakemake that I used throughout my internship. In this repo, aliases are set for the shell, and frequently used dependencies are installed.
NeuralPlexer -- A snakemake pipeline that uses Neuralplexer to predict Protein ligand interactions.
snakemake-tutorial -- A repository that contains an example pipeline for DNA read mapping between two sample types. Made for the Snakemake seminar.
distance-map -- A python script that analyses possible contacts between subunits of a protein complex and output contacts maps for each interface, and a subunit interaction graph.
LLPS-prediction -- A snakemake pipeline to annotate uniprot proteomes with scores from the PSPhunter and Seq2Phase tools.
LLPS-analysis -- A snakemake pipeline that analyses the performance of recently published LLPS prediction tools.
complex-prediction -- A snakemake pipeline to predict protein protein complexes using the Combfold algorithm.
yeast-computational-pi-screen -- Analysis of Humphreys et al 2021
Presentations and talks
Snakemake seminar -- My presentation to introduce snakemake to the AG Walther department . Repo hosted here.
Final presentation -- Presentation of my findings. Repo hosted here
Description of the dataset
.
├── data
│ ├── main
│ │ ├── cluster-channeling
│ │ │ ├── store.ttl
│ │ │ ├── UP000005640
│ │ │ └── UP000006548
│ │ └── contact-channeling
│ │ ├── 2024-06-02-combfold-glycolysis
│ │ ├── 2024-06-10-combfold-glycolysis
│ │ ├── 2024-06-13-alpha-fold-glycolysis
│ │ ├── enolase-neural-plexer
│ │ ├── fold_2024_06_21_14_11_enolase
│ │ └── tca-cycle-metabolon
│ └── side
│ ├── folding-actin
│ │ └── 2024-06-04
│ ├── folding-IMDPH1
│ │ └── 2024-06-01
│ └── hd-zip
├── LICENSE
├── pixi.lock
├── pixi.toml
├── README.md
├── resources
│ └── rcsb
│ ├── 5TD9.pdb
│ └── download
├── results
│ └── metabolon-prediction
│ └── tm-scores
│ ├── af2_enolase
│ └── af3_enolase
└── workflow
├── envs
│ └── structure-comparison.yml
├── help.sh
├── help.txt
├── scripts
│ └── convert-cif-to-pdb.py
└── Snakefile
创建时间：
2024-10-17
