Huilin's Notebook
Bioinformarics
1.
Bio mining notes
1.1.
Taxonomy NCBI
1.2.
parse JSON
2.
Binder design
2.1.
preprocessing
2.2.
design
2.3.
pae_interaction score
2.4.
backbones filtering
2.5.
results
3.
Computational Protein
3.1.
Protein
3.2.
Protein Representation
3.3.
Environment Setup
3.4.
databases: PDB, Swiss-Prot, OMG_Prot50
3.5.
BLAST usage: BLASTp makeblastdb
3.6.
protein strcuture measurement
3.7.
fasta to mutated fasta .py
3.8.
sequence similarity .py
3.9.
foldseek usage
3.10.
MMseqs2 usage
3.11.
localcolabfold usage
3.12.
Encoding Sequences into Integer Representations Using K-mer Binary Mapping
3.13.
parasail in C usage
3.14.
Biopython
3.15.
unipressed.UniprotkbClient
3.16.
daliLite V5 usage
4.
PyMol
MLDL
5.
A Deep learning Neural Network from the scratch via Numpy/Pandas
Statistics
6.
Paird t-Test
7.
Bayesian inference
Random
8.
Shell Bash Slurm Command
9.
LaTex
10.
Python
11.
Visualization
11.1.
Drawing a plane perpendicular to a given line
11.2.
Plotly color
11.3.
Movies
12.
Hugo: Book theme
13.
Hugo
14.
resources
Contact
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Huilin's Book
parse JSON from foldseek search server
https://search.foldseek.com/search