Improving drug-target affinity prediction via feature fusion and knowledge distillation

Structure-Aware Multimodal Deep Learning for Drug–Protein Interaction Prediction

(2022) Penglei Wang et al.   Journal of Chemical Information and Modeling

On the Frustration to Predict Binding Affinities from Protein–Ligand Structures with Deep Neural Networks

(2022) Mikhail Volkov et al.   JOURNAL OF MEDICINAL CHEMISTRY

An effective self-supervised framework for learning expressive molecular global representations to drug discovery

(2021) Pengyong Li et al.   BRIEFINGS IN BIOINFORMATICS

Forman persistent Ricci curvature (FPRC)-based machine learning models for protein–ligand binding affinity prediction

(2021) JunJie Wee et al.   BRIEFINGS IN BIOINFORMATICS

Knowledge Distillation: A Survey

(2021) Jianping Gou et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

InteractionGraphNet: A Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein–Ligand Interaction Predictions

(2021) Dejun Jiang et al.   JOURNAL OF MEDICINAL CHEMISTRY

GEFA: Early Fusion Approach in Drug-Target Affinity Prediction

(2021) Tri Minh Nguyen et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments

(2020) Lifan Chen et al.   BIOINFORMATICS

LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening

(2020) Viet-Khoa Tran-Nguyen et al.   Journal of Chemical Information and Modeling

MolTrans: Molecular interaction transformer for drug target interaction prediction

(2020) Kexin Huang et al.   BIOINFORMATICS

A Comprehensive Survey on Graph Neural Networks

(2020) Zonghan Wu et al.   IEEE Transactions on Neural Networks and Learning Systems

Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery

(2019) Xin Yang et al.   CHEMICAL REVIEWS

Predicting Drug–Target Interaction Using a Novel Graph Neural Network with 3D Structure-Embedded Graph Representation

(2019) Jaechang Lim et al.   Journal of Chemical Information and Modeling

Improving the Virtual Screening Ability of Target-Specific Scoring Functions Using Deep Learning Methods

(2019) Dingyan Wang et al.   Frontiers in Pharmacology

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

(2019) Liangzhen Zheng et al.   ACS Omega

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

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

OUP accepted manuscript

(2018)   BIOINFORMATICS

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

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

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

(2018) Zixuan Cang et al.   PLoS Computational Biology

Comparative Assessment of Scoring Functions: The CASF-2016 Update

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

Performance of machine-learning scoring functions in structure-based virtual screening

(2017) Maciej Wójcikowski et al.   Scientific Reports

Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets

(2013) Matthias R. Bauer et al.   Journal of Chemical Information and Modeling

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS