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Patrick Bryant's Projects

afprofile icon afprofile

Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile

arcene icon arcene

A deep CNN for evaluating the ARCENE dataset

cfold icon cfold

Structure prediction of alternative protein conformations

cmm icon cmm

Code written at CMM

coevolve icon coevolve

A repository for performing coevolutionary analysis of large datasets.

covid19.github.io icon covid19.github.io

Supervised machine learning for decoposing decision making in the COVID19 outbreak.

evobind icon evobind

In silico directed evolution of peptide binders with AlphaFold

gpt-2 icon gpt-2

Code for the paper "Language Models are Unsupervised Multitask Learners"

mhcii icon mhcii

Code for predicting the binding affinity of different MHC-II complexes to peptides of varying lengths in terms of ic50.

miga icon miga

MIGA is a Python package that provides a MSA (Multiple Sequence Alignment) mutual information genetic algorithm optimizer. It sorts two MSAs in a way that maximize or minimize their mutual information. The genetic algorithm solvers may run on both CPU and Nvidia GPUs.

molpc icon molpc

Modelling of Large Protein Complexes

oxmatch icon oxmatch

A simple script for matching sequences from two different MSAs based on the OX identifiers resulting from an hhblits search.

ptb_rnn icon ptb_rnn

A recurrent neural network of stacked LSTMs that predict text sequences using the Penn Treebank dataset.

speedppi icon speedppi

Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning

transpep icon transpep

Learning biological features of signal peptides with transformer neural networks.

umol icon umol

Protein-ligand structure prediction

xprize_covid icon xprize_covid

Predictor and Prescriptor models for the covid xprize challenge.

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