Huilin's Notebook
computational biology
1.
Binder design
1.1.
preprocessing
1.2.
design
1.3.
pae_interaction score
1.4.
backbones filtering
1.5.
results
2.
Bioinformatics
2.1.
Environment Setup
2.2.
Taxonomy NCBI
2.3.
parse JSON
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
2.17.
cif2pdb
2.18.
CD-HIT
2.19.
parse Blastp XML2
2.20.
batch alignment in chimeraX
Molecular Biology
3.
PyMol
4.
Gene
5.
Protein
MLDL
6.
A Deep learning Neural Network from the scratch via Numpy/Pandas
Statistics
7.
Paird t-Test
8.
Bayesian inference
Random
9.
Shell Bash Slurm Command
10.
Overleaf/Latx/Zotero
11.
Python
12.
Visualization
12.1.
Drawing a plane perpendicular to a given line
12.2.
Plotly color
12.3.
Movies
13.
mdbook usage
14.
Hugo: Book theme
15.
Hugo
16.
resources
Contact
World
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Rust
Coal
Navy
Ayu
Huilin's Book
Binder Design
target.pdb
preprocessing
binders design via RFdiffusion and ProteinMPNN-FastRelax
backbones filtering
pae_interaction score