mosayebi Goto Github PK

alphaflow

AlphaFold Meets Flow Matching for Generating Protein Ensembles

ampal

A simple, intuitive and Pythonic framework for representing biomolecular structure.

awsjupyter

This is a small tutorial to set up a jupyter notebook for data science and deep learning usign aws cloud services

chroma

A generative model for programmable protein design

colabdesign

Making Protein Design accessible to all via Google Colab!

colabfold

Making Protein folding accessible to all!

conf-gfn

confit

esm

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

evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

frame2seq

Structure-conditioned masked language modeling for protein sequence design

instructplm

The first large protein language model trained follows structure instructions.

isambard

Intelligent System for Analysis, Model Building And Rational Design of biomolecules.

jupyter-notebook-slides

lammps

Public development project of the LAMMPS MD software package

ligandmpnn

metl

Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models

metl-sim

High-throughput framework for running molecular simulations for METL

patchy_particle_simulation_lammps

patchydisc

This is an implementation of the Gaussian patchy disc model using the VMMC library of Lester Hedges.

prody

A Python Package for Protein Dynamics Analysis

protein_design_with_isambard

proteinmpnn

Code for the ProteinMPNN paper

pymol-color-alphafold

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

rf_diffusion_all_atom

Public RFDiffusionAA repo

rfdiffusion

Code for running RFdiffusion

rosettafold-all-atom

rosettafold2na

RoseTTAFold2 protein/nucleic acid complex prediction

umol

Protein-ligand structure prediction