erolic

Auto3D_pkg

Auto3D generates low-energy conformers from SMILES/SDF

PRIME

protein structure prediction with precision

a3fe

Automated Adaptive Absolute alchemical Free Energy calculator

mdigest

pySankey

create sankey diagrams with matplotlib

SINCHO-H2L

Pocket-to-Concavity

Pocket to Concavity is a tool for refinement of Protein-Ligand binding site shape from alpha-spheres

Native-contacts-determination-from-MD

We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU approach (http://pomalab.ippt.pan.pl/GoContactMap/).

CARA

Benchmarking compound activity prediction for real-world drug discovery applications

openmm-ml

High level API for using machine learning models in OpenMM simulations

Uni-Mol

Official Repository for the Uni-Mol Series Methods

AlphaRED

AlphaFold-initiated replica exchange protein docking

gnina

A deep learning framework for molecular docking

PROTACable

PROTACable is an end-to-end in-silico design toolkit for novel PROTACs

maize

A graph-based workflow manager for computational chemistry pipelines

ProtMamba-ssm

ProtMamba: a homology-aware but alignment-free protein state space model

PeptideBuilder

A simple Python library to generate model peptides

PocketAnchor

Learning Structure-based Pocket Representations for Protein-Ligand Interaction Prediction

pool

POOL (Peptide Optimization with Optimal Learning): code for "Discovering de novo peptide substrates for enzymes using machine learning"

PypKa

A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism

dimorphite_dl

Protonate Your SMILES! Mirror of https://git.durrantlab.pitt.edu/jdurrant/dimorphite_dl/

GrASP

Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention

arctic3d

Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

PRosettaC

gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

QSPRpred

A tool for creating Quantitative Structure Property Relationship (QSPR) models.

smina

QSARtuna

QSARtuna: QSAR model building with the optuna framework

applying-maths-book

Applying Maths in the Chemical and Biomolecular Sciences by Godfrey Beddard

binding-ddg-predictor

open source repository