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pyani_mmff

Python scripts to conduct optimization using a set of optimization algorithms utilizing an ANI energies and forces.

pyautofep

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

pydssp

A simplified implementation of DSSP algorithm for PyTorch and NumPy

pylipid

A python toolkit for analysing membrane protein-lipid interactions.

pythonmmgbsa

Program for running end point free energy calculations on protein-ligand complexes using AMBER and its associated MMPBSA.py program. Requires only a protein and ligand structure as input.

q6

Fork of Q. A program for understanding biomolecular properties with molecular dynamics under the hood.

qligfep

rdkit_blog

RDKit related blog posts, notebooks, and data.

rdkit_cpp

rdock

rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies.

rdpsovina

A fast docking tool with the random drift particle swarm optimization and based on the framework of AutoDock Vina and PSOVina

ref-alphafold-code

reinforced-genetic-algorithm

reinvent

reinvent4

A molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

relation

rf_diffusion_all_atom

Public RFDiffusionAA repo

rfdiffusion

Code for running RFdiffusion

rgn2

rl-graphinvent

RL-GraphINVENT is a platform for graph-based targeted molecular generation using graph neural networks and reinforcement learning. RL-GraphINVENT uses a Gated Graph Neural Network -based model fine-tuned using reinforcement learning to probabilistically generate new molecules with desired property profiles.

rosettafold

This package contains deep learning models and related scripts for RoseTTAFold

rosettafold-all-atom

rxdock

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout 2dd24cc after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

sbmolgen

scrubber

Enumerate conformational, protomeric, and pH-related microstates for docking with AutoDock

sdftosvg

Beautiful Molecule Renderer

secse

Systemic Evolutionary Chemical Space Exploration For Drug Discovery

selfies

Robust representation of semantically constrained graphs, in particular for molecules in chemistry

sencid

sire

Sire Molecular Simulations Framework