Oxford Protein Informatics Group

ANARCI

Antibody Numbering and Antigen Receptor ClassIfication

AbLang

AbLang: A language model for antibodies

DeLinker

ImmuneBuilder

Predict the structure of immune receptor proteins

AntiFold

Improved antibody structure-based design using inverse folding

DEVELOP

ABlooper

Tool for modelling the CDRs of antibodies

CaLM

Protein language model trained on coding DNA

Paragraph

Antibody paratope prediction using Graph Neural Networks with minimal feature vectors

dlab-public

Code for the paper "DLAB - Deep learning methods for structure-basedvirtual screening of antibodies"

DeepCoy

Graphinity

Graphinity: Equivariant Graph Neural Network Architecture for Predicting Change in Antibody-Antigen Binding Affinity

PLAbDab

The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures

kasearch

KA-Search: Rapid and exhaustive sequence identity search of known antibodies

AbLang2

An antibody-specific language model focusing on NGL prediction

SPACE2

Tool for rapid clustering of antibody models by the structure of their CDRs.

MolSnapper

PointVS

SE(3)-equivariant point cloud networks for virtual screening

binding-sites

SCALOP

Fragmenstein

Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse

OAS-CanonicalForms

Code to perform clustering of antibody CDRs from predicted structures of sequences from the Observed Antibody Space.

fragment_network_merges

Fragment merging using a graph database

cesped

Cryo-EM Supervised Pose Estimation Dataset utilities

sdAbs_vs_Abs

A comparison of the binding sites of antibodies and single-domain antibodies

hummus

Code associated with generating figures from Richardson & Binter et al, 2022.

molecular_rectifier

Given an RDKit molecule that does not sanitise, correct it until it does

Python_SmallWorld_API

An (unofficial) Python3 module to query the SmallWorld chemical space search server (https://sw.docking.org/search.html)

rdkit_to_params

Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file

Tz_her2_affinity_and_beyond

Design and refine high affinity antibody libraries