Flexible Artificial Intelligence Docking

hSTING-ExcB protein-ligand docking

mirror of https://gitlab.com/CaflischLab/SEED

Some shell functions to help scale and manage GOLD molecular docking jobs on an HPC

Automatic identification of important interactions and interaction-frequency-based scoring in protein-ligand complexes

PIAWeb - a graphical web interface for PIA

The NRGsuite is a PyMOL plugin (GUI) for FlexAID

NRGsuite is a PyMOL plugin (GUI) for FlexAID

Analysis on the number of non-hydrogen atomic contacts between a ligand and each of specified residues on the protein following molecular docking of multiple ligands to a protein structure.

Root-mean-square deviation of atomic positions

Repository for the Taba tool

Protein Recognition Index (PRI), measuring the similarity between H-bonding features in a given complex (predicted or designed) and the characteristic H-bond trends from crystallographic complexes

A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics

LigTMap currently supports prediction for 17 protein target classes that include 6000+ protein targets.

Flexible Artificial Intelligence Docking

Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.

A novel approach to pose selection in protein-ligand docking based on graph theory.

Colab version of "DiffDock: : Diffusion Steps, Twists, and Turns for Molecular Docking"

GaudiMM: A modular optimization platform for molecular design

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