Pinned Repositories
3DScience
MIT 20.S947 course on 3D scientific rendering
AF_Cluster
Predict multiple protein conformations using sequence clustering and AlphaFold2.
al-folio
A beautiful, simple, clean, and responsive Jekyll theme for academics
alphaflow
AlphaFold Meets Flow Matching for Generating Protein Ensembles
Enhanced_Sampling_Methods_Tutorials
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
football-project
Calculate surface tension of a "football" shape of actin using MC simulation
HP1paralogs-simulations
Scripts to run the simulations of HP1 paralogs
HPS-SS-model
HPS-SS model for IDPs
westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
TienMPhan's Repositories
TienMPhan/football-project
Calculate surface tension of a "football" shape of actin using MC simulation
TienMPhan/AF_Cluster
Predict multiple protein conformations using sequence clustering and AlphaFold2.
TienMPhan/al-folio
A beautiful, simple, clean, and responsive Jekyll theme for academics
TienMPhan/alphaflow
AlphaFold Meets Flow Matching for Generating Protein Ensembles
TienMPhan/Awesome-Diffusion-Models
A collection of resources and papers on Diffusion Models
TienMPhan/HP1paralogs-simulations
Scripts to run the simulations of HP1 paralogs
TienMPhan/CHEM101.6
TienMPhan/CmuMD
CmuMD implementation for PLUMED2
TienMPhan/CSpred
UCBShift is a program for predicting chemical shifts for backbone atoms and β-carbon of a protein in solution. It utilizes a machine learning module that makes predictions from features extracted from the 3D structures of the proteins.
TienMPhan/deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
TienMPhan/deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
TienMPhan/ELViM
ELViM is a method for visualizing the energy landscapes of biomolecules simulations.
TienMPhan/FRETpredict
Software for the prediction of FRET data from conformational ensembles.
TienMPhan/idpGPT
GPT models of PLMs trained to generate novel protein sequences when supplied with a prompt
TienMPhan/idpsam
Generate intrinsically disordered peptide conformations via machine learning
TienMPhan/led3score
TienMPhan/making-it-rain
Cloud-based molecular simulations for everyone
TienMPhan/MATILDA.FT
TienMPhan/MD_and_NMR_Relaxometry
TienMPhan/micrograd
A tiny scalar-valued autograd engine and a neural net library on top of it with PyTorch-like API
TienMPhan/msmbuilder2022
Statistical models for biomolecular dynamics
TienMPhan/msmhelper
Helper function for Markov State Models
TienMPhan/NeuralPLexer
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
TienMPhan/nmrdata
TienMPhan/paper-qa
LLM Chain for answering questions from documents with citations
TienMPhan/progen
Official release of the ProGen models
TienMPhan/pyDR
New implementation of pyDIFRATE
TienMPhan/pyDR_tutorial
Tutorial files for pyDR
TienMPhan/seekr2
Simulation-Enabled Estimation of Kinetic Rates - Version 2
TienMPhan/system-design-primer
Learn how to design large-scale systems. Prep for the system design interview. Includes Anki flashcards.