Wang-Lin-boop/PPI-Miner

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Created about 3 years ago
Updated over 1 year ago

Wang-Lin-boop/PPI-Miner

Wang-Lin-boop

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A Motif-Based PPI Searching Pipeline for PPI Mining and Protein Design

CADD-Scripts

Scripts for virtual screening, cross docking and protein relax using Schrödinegr and Rosetta

AutoMD

Easy to get started with molecular dynamics simulation.

GetPDB

Download pdb/protein structures using Uniprot id; This script will download related PDB files, extract chains(Optional), remove duplicates(Optional, maybe lost some conformation changed structures) and save as "UniprotID-PDBID-ModelID-ChainID.pdb/cif".

GeminiMol

Incorporation of conformational space profile into molecular representation learning, and its application to drug discovery, including virtual screening, target identification, and QSAR.

AlphaFoldDB_Processing

This script can clean up the disordered region in the AlphaFold DB structures to adapt it to the molecular docking, extract the sequence of the disordered region to make it available for sequence motif searching.

Biodb-Search

A user-friendly biomedical database integration interface.

CADD_Visual_Inspection_Training

Training data for visual inspection after structure-based virtual screening.

HPC_Monitor

Automatic monitoring of HPC information and Send warning information by E-mail.

Mutation_ddG_dataset

Wang-Lin-boop

My GitHub profile.

Rosetta-BashScript

Making Rosetta easier to use.

Linker-Design

Scripts for designing proximity-inducing compounds (PICs, including PROTACs, LYTACs) that generate linkers between ligands through the independent structure of a given two protein-ligand complex structures or the complex structure.