Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design

OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells

(2021) Zechen Wang et al.   Frontiers in Chemistry

A Deep Learning Approach to Antibiotic Discovery

(2020) Jonathan M. Stokes et al.   CELL

RosENet: Improving Binding Affinity Prediction by Leveraging Molecular Mechanics Energies with an Ensemble of 3D Convolutional Neural Networks

(2020) Hussein Hassan-Harrirou et al.   Journal of Chemical Information and Modeling

graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein–Ligand Complexes

(2020) Dmitry S. Karlov et al.   ACS Omega

Generative Network Complex for the Automated Generation of Drug-like Molecules

(2020) Kaifu Gao et al.   Journal of Chemical Information and Modeling

Extended connectivity interaction features: improving binding affinity prediction through chemical description

(2020) Norberto Sánchez-Cruz et al.   BIOINFORMATICS

DeepChemStable: Chemical Stability Prediction with an Attention-Based Graph Convolution Network

(2019) Xiuming Li et al.   Journal of Chemical Information and Modeling

AGL-Score: Algebraic Graph Learning Score for Protein–Ligand Binding Scoring, Ranking, Docking, and Screening

(2019) Duc Duy Nguyen et al.   Journal of Chemical Information and Modeling

Molecule Property Prediction Based on Spatial Graph Embedding

(2019) Xiaofeng Wang et al.   Journal of Chemical Information and Modeling

Atom table convolutional neural networks for an accurate prediction of compounds properties

(2019) Shuming Zeng et al.   npj Computational Materials

OnionNet: a Multiple-Layer Intermolecular-Contact-Based Convolutional Neural Network for Protein–Ligand Binding Affinity Prediction

(2019) Liangzhen Zheng et al.   ACS Omega

Spectral gap bounds for the simplicial Laplacian and an application to random complexes

(2019) Samir Shukla et al.   JOURNAL OF COMBINATORIAL THEORY SERIES A

Development and evaluation of a deep learning model for protein–ligand binding affinity prediction

(2018) Marta M Stepniewska-Dziubinska et al.   BIOINFORMATICS

Compound-protein Interaction Prediction with End-to-end Learning of Neural Networks for Graphs and Sequences

(2018) Masashi Tsubaki et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Improving classical scoring functions using random forest: The non-additivity of free energy terms’ contributions in binding

(2018) Karim Afifi et al.   Chemical Biology & Drug Design

Machine learning in chemoinformatics and drug discovery

(2018) Yu-Chen Lo et al.   DRUG DISCOVERY TODAY

Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks

(2018) Kedi Wu et al.   Journal of Chemical Information and Modeling

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

(2018) José Jiménez et al.   Journal of Chemical Information and Modeling

TopP -S : Persistent homology-based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility

(2018) Kedi Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Visualizing convolutional neural network protein-ligand scoring

(2018) Joshua Hochuli et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

(2018) Zixuan Cang et al.   PLoS Computational Biology

Development of a Protein-Ligand Extended Connectivity (PLEC) fingerprint and its application for binding affinity predictions

(2018) Maciej Wójcikowski et al.   BIOINFORMATICS

Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges

(2018) Duc Duy Nguyen et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data

(2018) Fergus Imrie et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions: The CASF-2016 Update

(2018) Minyi Su et al.   Journal of Chemical Information and Modeling

PotentialNet for Molecular Property Prediction

(2018) Evan N. Feinberg et al.   ACS Central Science

Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction

(2017) Zixuan Cang et al.   International Journal for Numerical Methods in Biomedical Engineering

Rigidity Strengthening: A Mechanism for Protein–Ligand Binding

(2017) Duc D. Nguyen et al.   Journal of Chemical Information and Modeling

Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction

(2017) Youjun Xu et al.   Journal of Chemical Information and Modeling

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction

(2017) Connor W. Coley et al.   Journal of Chemical Information and Modeling

Breaking the polar-nonpolar division in solvation free energy prediction

(2017) Bao Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

(2017) Zixuan Cang et al.   PLoS Computational Biology

Boosting Docking-Based Virtual Screening with Deep Learning

(2016) Janaina Cruz Pereira et al.   Journal of Chemical Information and Modeling

Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies

(2016) Bao Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular graph convolutions: moving beyond fingerprints

(2016) Steven Kearnes et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Random walks on simplicial complexes and harmonics

(2016) Sayan Mukherjee et al.   RANDOM STRUCTURES & ALGORITHMS

Simplicial complexes: Spectrum, homology and random walks

(2016) Ori Parzanchevski et al.   RANDOM STRUCTURES & ALGORITHMS

Classification of Current Scoring Functions

(2015) Jie Liu et al.   Journal of Chemical Information and Modeling

Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets

(2015) Hongjian Li et al.   Molecular Informatics

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

Spectra of combinatorial Laplace operators on simplicial complexes

(2013) Danijela Horak et al.   ADVANCES IN MATHEMATICS

ChemoPy: freely available python package for computational biology and chemoinformatics

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules

(2013) Alessandro Lusci et al.   Journal of Chemical Information and Modeling

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling