Pinned Repositories
Add-missing-Residues-to-PDB-files
Add missing residue to pdb files
AtomicFrustratometer_Results
Results for atomic frustratometer manuscript.
Attentive-Neural-Protein-Structure-Prediction
Prediction of protein tertiary structure via the “translation” of amino acid sequences into internal torsional angles.
beta-barrel-oligomerization
Code for the Vik Nanda lab's study of beta barrels, focusing on prediction of oligomerization
cluspro-tools
Provides tools for analyzing ClusPro protein docking results
deepdist
Deep learning prediction of protein residue-residue distances
DIPS
Database of Interacting Protein Structures (DIPS)
PackingFrustration_Refinement
Atomic packing frustratometer using Rosetta
SAGERank
SAGERank: Inductive Learning of Protein-Protein Interaction from Antibody-Antigen Recognition using Graph Sample and Aggregate Networks Framework
SARS2_RBD_Ab_escape_maps
Interactive visualization of deep mutational scanning maps of mutations to SARS-CoV-2 RBD that escape antibody or sera binding
Mingchenchen's Repositories
Mingchenchen/Add-missing-Residues-to-PDB-files
Add missing residue to pdb files
Mingchenchen/antibodyDesignLegacy
Mingchenchen/AWSEM
Mingchenchen/awsemmd_script
Mingchenchen/BetaSerpentine
Mingchenchen/Contact_map_prediciton_papers
A collection of all existing contact map prediciton papers.
Mingchenchen/Data_Management
Mingchenchen/dca-frustratometer
Code/files for the DCA frustratometer
Mingchenchen/DeepAlign
DeepAlign: the protein structure analysis toolkit
Mingchenchen/DeepFold
A deep learning frame for RNA structure prediction.
Mingchenchen/forcebalance
Systematic force field optimization.
Mingchenchen/frustratometer2
This repository contains the pipeline for running the frustratometer software
Mingchenchen/Frustratometer_tools
Mingchenchen/homework3
MATLAB code for ridge regression
Mingchenchen/LAMMPS-CHARMM-helper-scripts
Python scripts to handle some LAMMPS-CHARMM script differences.
Mingchenchen/mabbot
Generates a random name for an antibody-based drug
Mingchenchen/miRNA-target-prediction-papers
A collection of all existing miRNA target gene prediction papers
Mingchenchen/pdb-tools
Set of utility scripts to manipulate PDB files
Mingchenchen/ProDy-website
ProDy Website
Mingchenchen/Protein-Side-Chain-Packing-Problem
Protein Side Chain Packing Problem
Mingchenchen/protein_origami
Design platform for creating single-chain polyhedral cages made from coiled-coil building modules
Mingchenchen/Ridge-Regression-Models
Linear and Kernel Ridge regression
Mingchenchen/rwos
R interface to Web of Science Web Services API
Mingchenchen/stanford-tensorflow-tutorials
This repository contains code examples for the course CS 20SI: TensorFlow for Deep Learning Research.
Mingchenchen/TCR-pMHC
Note: Please download and unzip the "TCR-pMHC" file. Start using the database by opening the "index.html" file in a web browser. // The TCR-pMHC has been constructed by a grade 10 high school student from Vancouver, BC. This project attempts to produce a new database that stores information on T cells that target cancer cells and their interactions identified by researchers around the world. Since the number of known TCR-pMHC interactions are low, it can be inconvenient for researchers to gather data on TCRs that can recognize the target epitope and can slow down the progress of the research as well. This database allows researchers to learn about various TCRs and progress farther with these T cells. It also gives in depth profiles of the TCRs, allowing researchers to use techniques to reproduce T cells with receptors that can kill cancer cells within a patient.
Mingchenchen/the-talks
Mingchenchen/topo-ff
Parametrize a LAMMPS data file with a CHARMM force field
Mingchenchen/Upside-MD
Coarse-grained molecular dynamics for protein physics
Mingchenchen/VoronoiAnalysis
Python code that can be used to analyze molecular dynamics simulations of proteins/polymers solvated in water. The first and second hydration shells are calculated, the molecular volume, the partial molar volume, and the number of waters associated with each side chain are calculated. This is specifically for PNIPAM but can be modified fairly easily to suit other polymers/protiens. The MDAnalysis library is used for parsing trajectories. Voronio polygons are created using the pyvoro wrapper of Voro++.
Mingchenchen/VSS
Virtual Substitution Scan -- a plugin for VMD plateform