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alphafold_installation

The following is a step-by-step guide to install the alphafold 2 on an AWS EC2 Ubuntu instance

annotate_v

Antibody Annotation - Annotate VH and VL sequences (FR and CDR) in Python

annotate_v-for-pymol

Antibody Annotation - Annotate antibody VH and VL sequences (FR and CDR) in Pymol

antibody-csv-to-html

Javascript to convert antibody information from csv tables to html pages

bionemo-gitbook

bionemo_example_molecule_hts

Example workflow of small molecule virtual screening using BioNeMo containers

bvp_manuscript

Code for BVP manuscript

cas

List of my volunteer projects at the Chinese Antibody Society. https://xinyu-dev.github.io/cas/

cas-analytics-dashboard

An analytics dashboard built using Plotly Dash (Python) for data visualization of Chinese Antibody Society's multimedia platforms.

cas-collaboration

Collaborative projects for the Chinese Antibody Society

cas-covid-mab-tracker

Python script using API of ClincialTrials.gov to retrieve therapeutic antibodies for the COVID-19 Antibody Tracker of the Chinese Antibody Society. Tracker: https://chineseantibody.org/covid-19-track/

country-json

A simple data of the world by country each in JSON format.

general-image-processing

A collection of Python scripts for batch-processing images and facial recognition. 1) “Logo Resizer”: dynamically resizes images to fit bounding box. 2) “Headshot Cropper”: identifies faces using CV2, then extracts faces into round thumbnail images and resizes them. 3) “Volunteer Certificate”: reads data from CSV, dynamically resizes text to fit bounding box, then applies text style, and outputs image as pdf

hopp-woods

Prediction of hydrophilicity & antigenic determinants from protein sequences

igblast

Detailed explanation on how to setup database for NCBI IgBlast executable, and using it in Python

interactive-datatable

Simple implementation of a responsive, interactive data table using jquery, dataTables.js, and bootstrap. https://xinyu-dev.github.io/interactive-datatable/

mhci-a0201-9mer

Benchmarking MHC-I epitope prediction algorithms ( IEDB ANN, MHCFlurry, and NetMHCpan-BA) in prediction of high affinity (IC50 < 500 nM) 9-mer binders to human MHC-I HLA-A02:01.

patentseq

Converts image protein sequences in patents (3-letter coded) to 1-letter coded fasta format

plotly.py

An open-source, interactive graphing library for Python (includes Plotly Express) :sparkles:

pymol-script-repo

Collected scripts for Pymol

signal_peptide_mutagensis

repository for signal peptide mutagenesis paper

swot

Identify email addresses or domains names that belong to colleges or universities. Help automate the process of approving or rejecting academic discounts.

transmhcii

Code repository for manuscript: TransMHCII: a novel MHC-II binding prediction model built using a protein language model and an image classifier

world.geo.json

Annotated geo-json geometry files for the world

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