sokrypton/AM216

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sokrypton/AM216

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Material for lecture

ColabFold

Making Protein folding accessible to all!

Jupyter Notebook

ColabDesign

Making Protein Design accessible to all via Google Colab!

GREMLIN_CPP

GREMLIN - learn MRF/potts model from input multiple sequence alignment! Implementation now available in C++ and Tensorflow/Python!

Jupyter Notebook

af2bind

Jupyter Notebook

map_align

Contact map alignment

af_backprop

seqmodels

Jupyter Notebook

ColabBio

random colab notebooks for biology

Jupyter Notebook

GREMLIN

GREMLIN is a method to learn a statistical model of a protein family that captures both conservation and co-evolution patterns in the family. The strength of measured co-evolution is strongly predictive of residue-residue contacts in the 3D structure of the protein.

tf_proteins

some tools for working with protein (PDB) files in tensorflow

Jupyter Notebook

seqsal

Jupyter Notebook

algosb_2021

for algosb workshop

Jupyter Notebook

TrDesign_partialhall

TrDesign w/ Partial Hallucination support

laxy

lazy wrapper around jax

Jupyter Notebook

sp_deli

Jupyter Notebook

HelixFold

roscon2024

Jupyter Notebook

GREMLIN_LH

Jupyter Notebook

e2e

seqsal_v2

GREMLIN_CNN

Jupyter Notebook

EMBOIntegModelling23

Jupyter Notebook

AfDesign_partial

Jupyter Notebook

trdesign-motif

Codebase for our preprint using trRosetta to design proteins with discontinuous functional sites, found here: https://www.biorxiv.org/content/10.1101/2020.11.29.402743v1.abstract

ws2023

Jupyter Notebook

casp15_analysis

Jupyter Notebook

AccAdam_TF2

TF2-compatible Accumulated Gradients for Adam