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abangle

A tool for calculating and analysing the VH-VL orientation in antibodies.

ablm

Protein language model customized for antibodies

abs-scan

Alanine binding site scanning mutagenesis for evaluting the contribution of individual residues at the binding site towards small-molecule ligand recognition

absolut

Unconstrained lattice antibody-antigen bindings generator

alphafold

Open source code for AlphaFold.

annotate_v

Antibody Annotation - Annotate VH and VL sequences (FR and CDR) in Python

arpeggio

Calculation of interatomic interactions in molecular structures

biophi

BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.

biopython

Official git repository for Biopython (originally converted from CVS)

codes_for_foldx

some useful codes for foldx

codon_optimization

deeph3-distances-orientations

deeprank

Deep Learning for the ranking of protein-protein conformations

dligand2

dock2d

Dock2D: Synthetic datasets for the molecular recognition problem

dockq

DockQ is a single continuous quality measure for protein docked models based on the CAPRI evaluation protocol

druid

A pipeline for reproducible transcriptome-wide measurements of mRNA stability

dynamics

Dynamics PyMOL Plugin

efficient-evolution

Efficient evolution from protein language models

elaspic2

Predicting the effect of mutations on protein stability and protein binding affinity using pretrained neural networks and a ranking objective function.

enlighten2

Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems

esm

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

evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

flex_ddg_tutorial

gmx_tutorials_livecoms

LiveCoMS GROMACS Tutorials Paper

gnina

A deep learning framework for molecular docking

googletest

Googletest - Google Testing and Mocking Framework

graphppis

graphsol

A Protein Solubility Predictor developed by Graph Convolutional Network and Predicted Contact Map

gromacs

Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.