Identification of drug–target interaction from interactome network with ‘guilt-by-association’ principle and topology features

Novel Scaffold Fingerprint (SFP): Applications in Scaffold Hopping and Scaffold-Based Selection of Diverse Compounds

(2015) Obdulia Rabal et al.   Journal of Chemical Information and Modeling

Toward more realistic drug-target interaction predictions

(2014) T. Pahikkala et al.   BRIEFINGS IN BIOINFORMATICS

AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins

(2014) Diogo Santos-Martins et al.   Journal of Chemical Information and Modeling

Systems Biology Brings New Dimensions for Structure-Based Drug Design

(2014) Jianfeng Pei et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Large-scale prediction of human kinase–inhibitor interactions using protein sequences and molecular topological structures

(2013) Dong-Sheng Cao et al.   ANALYTICA CHIMICA ACTA

Drug–target interaction prediction through domain-tuned network-based inference

(2013) Salvatore Alaimo et al.   BIOINFORMATICS

Similarity-based machine learning methods for predicting drug–target interactions: a brief review

(2013) Hao Ding et al.   BRIEFINGS IN BIOINFORMATICS

Quantifying the Fingerprint Descriptor Dependence of Structure–Activity Relationship Information on a Large Scale

(2013) Dilyana Dimova et al.   Journal of Chemical Information and Modeling

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

Predicting Drug-Target Interactions Using Drug-Drug Interactions

(2013) Shinhyuk Kim et al.   PLoS One

Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization

(2012) M. Gonen   BIOINFORMATICS

Drug–target interaction prediction by learning from local information and neighbors

(2012) Jian-Ping Mei et al.   BIOINFORMATICS

Network-based characterization of drug-regulated genes, drug targets, and toxicity

(2012) Max Kotlyar et al.   METHODS

Predicting drug targets based on protein domains

(2012) Yin-Ying Wang et al.   Molecular BioSystems

Drug–target interaction prediction by random walk on the heterogeneous network

(2012) Xing Chen et al.   Molecular BioSystems

HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores

(2012) Martin H. Schaefer et al.   PLoS One

Prediction of Chemical-Protein Interactions Network with Weighted Network-Based Inference Method

(2012) Feixiong Cheng et al.   PLoS One

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Gaussian interaction profile kernels for predicting drug–target interaction

(2011) Twan van Laarhoven et al.   BIOINFORMATICS

Chemoproteomic approaches to drug target identification and drug profiling

(2011) Marcus Bantscheff et al.   BIOORGANIC & MEDICINAL CHEMISTRY

An iterative approach of protein function prediction

(2011) Xiaoxiao Chi et al.   BMC BIOINFORMATICS

Identifying Compound-Target Associations by Combining Bioactivity Profile Similarity Search and Public Databases Mining

(2011) Tiejun Cheng et al.   Journal of Chemical Information and Modeling

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces

(2010) Zheng Xia et al.   BMC Systems Biology

PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints

(2010) Chun Wei Yap   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure of Protein Interaction Networks and Their Implications on Drug Design

(2009) Takeshi Hase et al.   PLoS Computational Biology

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces

(2008) Y. Yamanishi et al.   BIOINFORMATICS

Quantitative systems-level determinants of human genes targeted by successful drugs

(2007) L. Yao et al.   GENOME RESEARCH