DeepAffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks

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

(2018) José Jiménez 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

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

(2017) Yunan Luo et al.   Nature Communications

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

(2017) Zixuan Cang et al.   PLoS Computational Biology

Effectively identifying compound-protein interactions by learning from positive and unlabeled examples

(2016) Zhanzhan Cheng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Boosting compound-protein interaction prediction by deep learning

(2016) Kai Tian et al.   METHODS

A comprehensive map of molecular drug targets

(2016) Rita Santos et al.   NATURE REVIEWS DRUG DISCOVERY

RaptorX-Property: a web server for protein structure property prediction

(2016) Sheng Wang et al.   NUCLEIC ACIDS RESEARCH

Drug–target interaction prediction: databases, web servers and computational models

(2015) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

HMMER web server: 2015 update

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening

(2015) Qurrat Ul Ain et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

(2014) C. N. Magnan et al.   BIOINFORMATICS

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Genomics-Enabled Drug Repositioning and Repurposing

(2014) Aidan Power et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Predicting drug-target interactions using restricted Boltzmann machines

(2013) Yuhao Wang et al.   BIOINFORMATICS

Scalable prediction of compound-protein interactions using minwise hashing

(2013) Yasuo Tabei et al.   BMC Systems Biology

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

PDBsum additions

(2013) Tjaart A. P. de Beer et al.   NUCLEIC ACIDS RESEARCH

Rational Approaches to Improving Selectivity in Drug Design

(2012) David J. Huggins et al.   JOURNAL OF MEDICINAL CHEMISTRY

Prediction of chemical–protein interactions: multitarget-QSAR versus computational chemogenomic methods

(2012) Feixiong Cheng et al.   Molecular BioSystems

A Systematic Prediction of Multiple Drug-Target Interactions from Chemical, Genomic, and Pharmacological Data

(2012) Hua Yu et al.   PLoS One

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

(2010) Roger L. Chang et al.   PLoS Computational Biology

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH