Huilin's Notebook
Bioinformarics
1.
Binder design
1.1.
preprocessing
1.2.
design
1.3.
pae_interaction score
1.4.
backbones filtering
1.5.
results
2.
Computational Protein
2.1.
Protein
2.2.
Protein Representation
2.3.
Environment Setup
2.4.
databases: PDB, Swiss-Prot, OMG_Prot50
2.5.
BLAST usage: BLASTp makeblastdb
2.6.
protein strcuture measurement
2.7.
fasta to mutated fasta .py
2.8.
sequence similarity .py
2.9.
foldseek usage
2.10.
MMseqs2 usage
2.11.
localcolabfold usage
2.12.
Encoding Sequences into Integer Representations Using K-mer Binary Mapping
2.13.
parasail in C usage
2.14.
Biopython
2.15.
unipressed.UniprotkbClient
2.16.
daliLite V5 usage
3.
PyMol
MLDL
4.
A Deep learning Neural Network from the scratch via Numpy/Pandas
Statistics
5.
Bayesian inference
Random
6.
Shell Bash Slurm Command
7.
LaTex
8.
Python
9.
Visualization
9.1.
Drawing a plane perpendicular to a given line
9.2.
Plotly color
9.3.
Movies
10.
Hugo: Book theme
11.
Hugo
12.
resources
Contact
World
Light
Rust
Coal
Navy
Ayu
Huilin's Book
Protein visual representation
ref: https://pdb101.rcsb.org/learn/videos
Space-filling diagram:
shows all atoms
Ribbon/Cartoon diagram:
shows the protein backbone and highlights the alpha helices.
Surface diagram:
shows areas that are accessible to water molecules.
