Related references
Note: Only part of the references are listed.Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities
Marinka Zitnik et al.
INFORMATION FUSION (2019)
Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning
Mahendra Awale et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
Predictive approaches for drug combination discovery in cancer
Seyed Ali Madani Tonekaboni et al.
BRIEFINGS IN BIOINFORMATICS (2018)
Recent applications of machine learning in medicinal chemistry
Jane Panteleev et al.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2018)
Machine learning in chemoinformatics and drug discovery
Yu-Chen Lo et al.
DRUG DISCOVERY TODAY (2018)
The rise of deep learning in drug discovery
Hongming Chen et al.
DRUG DISCOVERY TODAY (2018)
In silico identification of drug target pathways in breast cancer subtypes using pathway cross-talk inhibition
Claudia Cava et al.
JOURNAL OF TRANSLATIONAL MEDICINE (2018)
Current Concepts of Neurodegenerative Mechanisms in Alzheimer's Disease
Kasthuri Bai Magalingam et al.
BIOMED RESEARCH INTERNATIONAL (2018)
Machine Learning for Drug-Target Interaction Prediction
Ruolan Chen et al.
MOLECULES (2018)
Network-Based Methods for Prediction of Drug-Target Interactions
Zengrui Wu et al.
FRONTIERS IN PHARMACOLOGY (2018)
Computational Multitarget Drug Design
Weilin Zhang et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
An in silico strategy for identification of novel drug targets against Plasmodium falciparum
Subhashree Rout et al.
PARASITOLOGY RESEARCH (2017)
A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information
Yunan Luo et al.
NATURE COMMUNICATIONS (2017)
The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data
Mahendra Awale et al.
JOURNAL OF CHEMINFORMATICS (2017)
Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks
Mehrab Ghanat Bari et al.
SCIENTIFIC REPORTS (2017)
Application of the Subtractive Genomics and Molecular Docking Analysis for the Identification of Novel Putative Drug Targets against Salmonella enterica subsp enterica serovar Poona
Tanvir Hossain et al.
BIOMED RESEARCH INTERNATIONAL (2017)
Target-similarity search using Plasmodium falciparum proteome identifies approved drugs with anti-malarial activity and their possible targets
Reagan M. Mogire et al.
PLOS ONE (2017)
MOST: most-similar ligand based approach to target prediction
Tao Huang et al.
BMC BIOINFORMATICS (2017)
Leveraging Big Data to Transform Target Selection and Drug Discovery
B. Chen et al.
CLINICAL PHARMACOLOGY & THERAPEUTICS (2016)
Current state and challenges for dynamic metabolic modeling
Eleni Vasilakou et al.
CURRENT OPINION IN MICROBIOLOGY (2016)
Descriptors and their selection methods in QSAR analysis: paradigm for drug design
Danishuddin et al.
DRUG DISCOVERY TODAY (2016)
Using reverse docking for target identification and its applications for drug discovery
Aeri Lee et al.
EXPERT OPINION ON DRUG DISCOVERY (2016)
Precision medicine, genomics and drug discovery
Lon R. Cardon et al.
HUMAN MOLECULAR GENETICS (2016)
Improving chemical similarity ensemble approach in target prediction
Zhonghua Wang et al.
JOURNAL OF CHEMINFORMATICS (2016)
A theoretical study on predicted protein targets of apple polyphenols and possible mechanisms of chemoprevention in colorectal cancer
Bernardina Scafuri et al.
SCIENTIFIC REPORTS (2016)
Computational approaches in target identification and drug discovery
Theodora Katsila et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2016)
Large-scale exploration and analysis of drug combinations
Peng Li et al.
BIOINFORMATICS (2015)
Panel docking of small-molecule libraries - Prospects to improve efficiency of lead compound discovery
Pakornwit Sarnpitak et al.
BIOTECHNOLOGY ADVANCES (2015)
Machine-learning approaches in drug discovery: methods and applications
Antonio Lavecchia
DRUG DISCOVERY TODAY (2015)
Improvements, trends, and new ideas in molecular docking: 2012-2013 in review
Elizabeth Yuriev et al.
JOURNAL OF MOLECULAR RECOGNITION (2015)
Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens
Yu-Chen Lo et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
In silico Prediction of Drug Metabolism by P450
Carolina H. Andrade et al.
CURRENT DRUG METABOLISM (2014)
Genomics and transcriptomics in drug discovery
Joaquin Dopazo
DRUG DISCOVERY TODAY (2014)
Activity cliffs in drug discovery: Dr Jekyll or Mr Hyde?
Maykel Cruz-Monteagudo et al.
DRUG DISCOVERY TODAY (2014)
Reverse docking: a powerful tool for drug repositioning and drug rescue
Prashant S. Kharkar et al.
FUTURE MEDICINAL CHEMISTRY (2014)
SwissTargetPrediction: a web server for target prediction of bioactive small molecules
David Gfeller et al.
NUCLEIC ACIDS RESEARCH (2014)
Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus
Daniel Reker et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4)
Ryan T. Cameron et al.
BIOCHEMICAL PHARMACOLOGY (2013)
HitPick: a web server for hit identification and target prediction of chemical screenings
Xueping Liu et al.
BIOINFORMATICS (2013)
Calmodulin as a Potential Target by Which Berberine Induces Cell Cycle Arrest in Human Hepatoma Bel7402 Cells
Chao Ma et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2013)
Network-Based Approaches in Drug Discovery and Early Development
J. M. Harrold et al.
CLINICAL PHARMACOLOGY & THERAPEUTICS (2013)
Relating Anatomical Therapeutic Indications by the Ensemble Similarity of Drug Sets
Leihong Wu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)
Machine Learning Prediction of Cancer Cell Sensitivity to Drugs Based on Genomic and Chemical Properties
Michael P. Menden et al.
PLOS ONE (2013)
Combining Machine Learning Systems and Multiple Docking Simulation Packages to Improve Docking Prediction Reliability for Network Pharmacology
Kun-Yi Hsin et al.
PLOS ONE (2013)
Inverse Virtual Screening allows the discovery of the biological activity of natural compounds
Gianluigi Lauro et al.
BIOORGANIC & MEDICINAL CHEMISTRY (2012)
Target discovery from data mining approaches
Yongliang Yang et al.
DRUG DISCOVERY TODAY (2012)
Large-scale prediction and testing of drug activity on side-effect targets
Eugen Lounkine et al.
NATURE (2012)
Three-dimensional reconstruction of protein networks provides insight into human genetic disease
Xiujuan Wang et al.
NATURE BIOTECHNOLOGY (2012)
TDR Targets: a chemogenomics resource for neglected diseases
Maria P. Magarinos et al.
NUCLEIC ACIDS RESEARCH (2012)
idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach
Jui-Chih Wang et al.
NUCLEIC ACIDS RESEARCH (2012)
The interprotein scoring noises in glide docking scores
Wei Wang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2012)
Large-scale reverse docking profiles and their applications
Minho Lee et al.
BMC BIOINFORMATICS (2012)
Contribution of microarray data to the advancement of knowledge on the Mycobacterium tuberculosis interactome: Use of the random partial least squares approach
Gaston K. Mazandu et al.
INFECTION GENETICS AND EVOLUTION (2011)
Robust Scoring Functions for Protein-Ligand Interactions with Quantum Chemical Charge Models
Jui-Chih Wang et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Inverse Virtual Screening of Antitumor Targets: Pilot Study on a Small Database of Natural Bioactive Compounds
Gianluigi Lauro et al.
JOURNAL OF NATURAL PRODUCTS (2011)
From in silico target prediction to multi-target drug design: Current databases, methods and applications
Alexios Koutsoukas et al.
JOURNAL OF PROTEOMICS (2011)
Link prediction in complex networks: A survey
Linyuan Lue et al.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS (2011)
Identifying Causal Genes and Dysregulated Pathways in Complex Diseases
Yoo-Ah Kim et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data
Xing-Ming Zhao et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
Pedro J. Ballester et al.
BIOINFORMATICS (2010)
TargetSpy: a supervised machine learning approach for microRNA target prediction
Martin Sturm et al.
BMC BIOINFORMATICS (2010)
Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis
Carola Huthmacher et al.
BMC SYSTEMS BIOLOGY (2010)
Selectively Nonselective Kinase Inhibition: Striking the Right Balance
Richard Morphy
JOURNAL OF MEDICINAL CHEMISTRY (2010)
Target Fishing for Chemical Compounds Using Target-Ligand Activity Data and Ranking Based Methods
Nikil Wale et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
Predicting new molecular targets for known drugs
Michael J. Keiser et al.
NATURE (2009)
Walking the interactome for prioritization of candidate disease genes
Sebastian Koehler et al.
AMERICAN JOURNAL OF HUMAN GENETICS (2008)
targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis
Karthik Raman et al.
BMC SYSTEMS BIOLOGY (2008)
Ligand-Target Prediction Using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics
Florian Nigsch et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2008)
Quantifying the relationships among drug classes
Jerome Hert et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2008)
Network-based global inference of human disease genes
Xuebing Wu et al.
MOLECULAR SYSTEMS BIOLOGY (2008)
Network pharmacology: the next paradigm in drug discovery
Andrew L. Hopkins
NATURE CHEMICAL BIOLOGY (2008)
SuperPred:: drug classification and target prediction
Mathias Dunkel et al.
NUCLEIC ACIDS RESEARCH (2008)
Drug target identification using side-effect similarity
Monica Campillos et al.
SCIENCE (2008)
Turning promiscuous kinase inhibitors into safer drugs
Xi Zhang et al.
TRENDS IN BIOTECHNOLOGY (2008)
Inferring Pathway Activity toward Precise Disease Classification
Eunjung Lee et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
STITCH: interaction networks of chemicals and proteins
Michael Kuhn et al.
NUCLEIC ACIDS RESEARCH (2008)
Network-based classification of breast cancer metastasis
Han-Yu Chuang et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties
Chloe-Agathe Azencott et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)
Relating protein pharmacology by ligand chemistry
Michael J. Keiser et al.
NATURE BIOTECHNOLOGY (2007)
In silico pharmacology for drug discovery: applications to targets and beyond
S. Ekins et al.
BRITISH JOURNAL OF PHARMACOLOGY (2007)
Bridging chemical and biological space: Target fishing using 2D and 3D molecular descriptors
James H. Nettles et al.
JOURNAL OF MEDICINAL CHEMISTRY (2006)
A critical assessment of docking programs and scoring functions
Gregory L. Warren et al.
JOURNAL OF MEDICINAL CHEMISTRY (2006)
Peptide deformylase is a potential target for anti-Helicobacter pylori drugs:: Reverse docking, enzymatic assay, and X-ray crystallography validation
Jianhua Cai et al.
PROTEIN SCIENCE (2006)
Global mapping of pharmacological space
Gaia V. Paolini et al.
NATURE BIOTECHNOLOGY (2006)
TarFisDock: a web server for identifying drug targets with docking approach
Honglin Li et al.
NUCLEIC ACIDS RESEARCH (2006)
Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases
Nidhi et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2006)
Selective optimization of side activities: the SOSA approach
CG Wermuth
DRUG DISCOVERY TODAY (2006)
Can we rationally design promiscuous drugs?
AL Hopkins et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2006)
Computational models for predicting interactions with cytochrome p450 enzyme
Rieko Arimoto
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2006)
Artemisinin-based combinations
EA Ashley et al.
CURRENT OPINION IN INFECTIOUS DISEASES (2005)
Biospectra analysis: Model proteome characterizations for linking molecular structure and biological response
AF Fliri et al.
JOURNAL OF MEDICINAL CHEMISTRY (2005)
Biological spectra analysis: Linking biological activity profiles to molecular structure
AF Fliri et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia
BL Roth et al.
NATURE REVIEWS DRUG DISCOVERY (2004)
Clustering of interval data based on city-block distances
RMCR de Souza et al.
PATTERN RECOGNITION LETTERS (2004)
From magic bullets to designed multiple ligands
R Morphy et al.
DRUG DISCOVERY TODAY (2004)
Naive Bayesian classification of structured data
PA Flach et al.
MACHINE LEARNING (2004)
Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
J Hert et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2004)
Molecular similarity: a key technique in molecular informatics
A Bender et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2004)
Applying data mining techniques to library design, lead generation and lead optimization
DC Weaver
CURRENT OPINION IN CHEMICAL BIOLOGY (2004)
CLIP: Similarity searching of 3D databases using clique detection
N Rhodes et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2003)
The structure of the protein universe and genome evolution
EV Koonin et al.
NATURE (2002)
TTD: Therapeutic Target Database
X Chen et al.
NUCLEIC ACIDS RESEARCH (2002)
Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases
JW Raymond et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2002)
Drug design by machine learning: support vector machines for pharmaceutical data analysis
R Burbidge et al.
COMPUTERS & CHEMISTRY (2001)
PASS: prediction of activity spectra for biologically active substances
A Lagunin et al.
BIOINFORMATICS (2000)
Combinatorial preferences affect molecular similarity/diversity calculations using binary fingerprints and Tanimoto coefficients
JW Godden et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2000)