Molecular Docking

26 papers with code • 0 benchmarks • 0 datasets

Predicting the binding structure of a small molecule ligand to a protein, which is critical to drug design.

Description from: DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

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Use these libraries to find Molecular Docking models and implementations
2 papers
943

Most implemented papers

Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity

deepchem/deepchem 30 Mar 2017

The atomic convolutional neural network is trained to predict the experimentally determined binding affinity of a protein-ligand complex by direct calculation of the energy associated with the complex, protein, and ligand given the crystal structure of the binding pose.

SHREC 2022: Protein-ligand binding site recognition

lucagl/moad_ligandfinder 13 Jun 2022

This paper presents the methods that have participated in the SHREC 2022 contest on protein-ligand binding site recognition.

DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

gcorso/diffdock 4 Oct 2022

We instead frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses.

Using the Fast Fourier Transform in Binding Free Energy Calculations

nguyentrunghai/BPMFwFFT 27 Jul 2017

According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the ligand apo ensemble and a rigid receptor.

DeepAtom: A Framework for Protein-Ligand Binding Affinity Prediction

YanjunLi-CS/DeepAtom_SupplementaryMaterials 1 Dec 2019

The cornerstone of computational drug design is the calculation of binding affinity between two biological counterparts, especially a chemical compound, i. e., a ligand, and a protein.

DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representations

cansyl/DEEPScreen Chemical Science 2020

The identification of physical interactions between drug candidate compounds and target biomolecules is an important process in drug discovery.

Assigning Confidence to Molecular Property Prediction

aspuru-guzik-group/assessing_mol_prediction_confidence 23 Feb 2021

Introduction: Computational modeling has rapidly advanced over the last decades, especially to predict molecular properties for chemistry, material science and drug design.

DOCKSTRING: easy molecular docking yields better benchmarks for ligand design

dockstring/dockstring 29 Oct 2021

The field of machine learning for drug discovery is witnessing an explosion of novel methods.

Direct Molecular Conformation Generation

directmolecularconfgen/dmcg 3 Feb 2022

Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task in bioinformatics and pharmacology.

DEL-Dock: Molecular Docking-Enabled Modeling of DNA-Encoded Libraries

insitro/insitro-research 30 Nov 2022

Computational models have been deployed to learn the latent binding affinities that are correlated to the sequenced count data; however, this correlation is often obfuscated by various sources of noise introduced in its complicated data-generation process.