Mingchenchen

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/SAGERank

SAGERank: Inductive Learning of Protein-Protein Interaction from Antibody-Antigen Recognition using Graph Sample and Aggregate Networks Framework

Mingchenchen/Attentive-Neural-Protein-Structure-Prediction

Prediction of protein tertiary structure via the “translation” of amino acid sequences into internal torsional angles.

Mingchenchen/deepdist

Deep learning prediction of protein residue-residue distances

Mingchenchen/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/af2_conformations

A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2

Mingchenchen/af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

Mingchenchen/AttnPacker

Code and Pre-Trained Models for "AttnPacker: An end-to-end deep learning method for protein side-chain packing"

Mingchenchen/best-of-atomistic-machine-learning

🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.

Mingchenchen/CollepardoLab_Chromatin_Model

Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions".

Mingchenchen/cornell-cs5785-applied-ml

Teaching materials for the applied machine learning course at Cornell Tech

Mingchenchen/dgl-lifesci

Python package for graph neural networks in chemistry and biology

Mingchenchen/esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Mingchenchen/EvoClustRNA

RNA 3D structure prediction using multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io

Mingchenchen/ExpandedBenchmark

Mingchenchen/genie

De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds

Mingchenchen/gmx_makecyclictop

This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology file

Mingchenchen/GuthrieSolv

Experimental small molecule hydration free energy dataset

Mingchenchen/ibm3202

Google Colab Tutorials for IBM3202

Mingchenchen/manyfold

🧬 ManyFold: An efficient and flexible library for training and validating protein folding models

Mingchenchen/MCMG

MCMG_V1

Mingchenchen/p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

Mingchenchen/pensa

PENSA (Protein Ensemble Analysis) - a collection of python methods for exploratory analysis and comparison of protein structural ensembles.

Mingchenchen/phdthesis

Gaussian Processes and Statistical Decision-making in Non-Euclidean Spaces

Mingchenchen/plddt2csv

Extract the plddt value of Alphafold2 from .pkl to .csv file

Mingchenchen/pyFrustratometer

Google Colab/Python implementation of AWSEM frustratometer

Mingchenchen/qligfep

Mingchenchen/qml

Introductions to key concepts in quantum machine learning, as well as tutorials and implementations from cutting-edge QML research.

Mingchenchen/ref-Alphafold-Code

Mingchenchen/SNfold

The protein structure prediction software SNfold

Mingchenchen/TankBind

Open source code for TankBind. Galixir Tenchnologies