protein-ligand-docking

There are 23 repositories under protein-ligand-docking topic.

  • p2rank

    rdk/p2rank

    P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

    Language:Groovy23096131
  • awesome-molecular-docking

    Thinklab-SJTU/awesome-molecular-docking

    We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.

    88305

  • rxdock/rxdock

    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]

    Language:C++672019

  • insilichem/gaudi

    GaudiMM: A modular optimization platform for molecular design

    Language:Python327814

  • suneelbvs/DiffDock

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

    Language:Jupyter Notebook23306

  • rasbt/siteinterlock

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

    Language:Python19408

  • LDeng0205/confidence-bootstrapping

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

    Language:Python17212

  • NRGlab/FlexAID

    Flexible Artificial Intelligence Docking

    Language:C154011

  • ShirleyWISiu/LigTMap

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

    Language:Python13219

  • psa-lab/siteinterlock

    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

    Language:Python9204

  • rasbt/protein-recognition-index

    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

    Language:Python8305

  • azevedolab/taba

    Repository for the Taba tool

    Language:Python7002

  • neudinger/pyDockRMSD

    Root-mean-square deviation of atomic positions

    Language:C6122

  • YangLing0818/IRDiff

    [ICML 2024] Interaction-based Retrieval-augmented Diffusion Models for Protein-specific 3D Molecule Generation

    4

  • kevinshliu/Protein-Ligand-Interaction-Analysis

    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.

    Language:Python3101

  • lmorency/NRGsuite

    The NRGsuite is a PyMOL plugin (GUI) for FlexAID

    Language:Python3348

  • michabirklbauer/PIAWeb

    PIAWeb - a graphical web interface for PIA

    Language:Python3100

  • NRGlab/NRGsuite

    NRGsuite is a PyMOL plugin (GUI) for FlexAID

    Language:Python3403

  • manaakiwhenua/gold-functions

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

    Language:Lua120

  • michabirklbauer/protein_docking

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

    Language:Jupyter Notebook1110

  • drhuangwc/hSTING-ExcB-protein-ligand-docking

    hSTING-ExcB protein-ligand docking

    Language:Python00

  • lmorency/FlexAID

    Flexible Artificial Intelligence Docking

    Language:C0100

  • UnixJunkie/SEED-mirror

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

    Language:C++20