Oxford Protein Informatics Group

ANARCI

Antibody Numbering and Antigen Receptor ClassIfication

DeLinker

AbLang

AbLang: A language model for antibodies

ImmuneBuilder

Predict the structure of immune receptor proteins

DEVELOP

ABlooper

Tool for modelling the CDRs of antibodies

dlab-public

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

DeepCoy

Paragraph

Antibody paratope prediction using Graph Neural Networks with minimal feature vectors

AntiFold

Improved antibody structure-based design using inverse folding

CaLM

Protein language model trained on coding DNA

Graphinity

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

kasearch

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

PLAbDab

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

SPACE2

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

AbLang2

An antibody-specific language model focusing on NGL prediction

PointVS

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

binding-sites

MolSnapper

SCALOP

Fragmenstein

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

fragment_network_merges

Fragment merging using a graph database

OAS-CanonicalForms

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

cesped

Cryo-EM Supervised Pose Estimation Dataset utilities

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

sdAbs_vs_Abs

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

Tz_her2_affinity_and_beyond

Design and refine high affinity antibody libraries