Large‐scale prediction of drug–target relationships

[1]  S. Knapp,et al.  A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases , 2007, Proceedings of the National Academy of Sciences.

[2]  Christian von Mering,et al.  STITCH: interaction networks of chemicals and proteins , 2007, Nucleic Acids Res..

[3]  K. Dolinski,et al.  The BioGRID Interaction Database: 2008 update , 2007, Nucleic Acids Res..

[4]  Martin Serrano,et al.  Nucleic Acids Research Advance Access published October 18, 2007 ChemBank: a small-molecule screening and , 2007 .

[5]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[6]  Robert B. Russell,et al.  SuperTarget and Matador: resources for exploring drug-target relationships , 2007, Nucleic Acids Res..

[7]  Michael L. Creech,et al.  Integration of biological networks and gene expression data using Cytoscape , 2007, Nature Protocols.

[8]  A. Barabasi,et al.  Drug—target network , 2007, Nature Biotechnology.

[9]  Matthew Suderman,et al.  Tools for visually exploring biological networks , 2007, Bioinform..

[10]  D. Rognan.  Chemogenomic approaches to rational drug design , 2007, British journal of pharmacology.

[11]  Pierre Baldi,et al.  ChemDB update - full-text search and virtual chemical space , 2007, Bioinform..

[12]  C. Chong,et al.  New uses for old drugs , 2007, Nature.

[13]  R Abagyan,et al.  Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs , 2007, Proceedings of the National Academy of Sciences.

[14]  A. Bender,et al.  Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off‐Target Effects from Chemical Structure , 2007, ChemMedChem.

[15]  Gopal R. Gopinath,et al.  Reactome: a knowledge base of biologic pathways and processes , 2007, Genome Biology.

[16]  Pall I. Olason,et al.  A human phenome-interactome network of protein complexes implicated in genetic disorders , 2007, Nature Biotechnology.

[17]  Xi Zhang,et al.  Molecular basis for specificity in the druggable kinome : sequence-based analysis , 2007 .

[18]  Michael J. Keiser,et al.  Relating protein pharmacology by ligand chemistry , 2007, Nature Biotechnology.

[19]  E. Mardis,et al.  An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.

[20]  Y. Zhang,et al.  IntAct—open source resource for molecular interaction data , 2006, Nucleic Acids Res..

[21]  Xin Wen,et al.  BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities , 2006, Nucleic Acids Res..

[22]  Helen E. Parkinson,et al.  ArrayExpress—a public database of microarray experiments and gene expression profiles , 2006, Nucleic Acids Res..

[23]  Christian von Mering,et al.  STRING 7—recent developments in the integration and prediction of protein interactions , 2006, Nucleic Acids Res..

[24]  Z. Deng,et al.  Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors. , 2006, Journal of medicinal chemistry.

[25]  J. Nicholson.  Global systems biology, personalized medicine and molecular epidemiology , 2006, Molecular systems biology.

[26]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[27]  Inmar E. Givoni,et al.  Exploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast , 2006, Cell.

[28]  A. Fraser,et al.  Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways , 2006, Nature Genetics.

[29]  G. V. Paolini,et al.  Global mapping of pharmacological space , 2006, Nature Biotechnology.

[30]  C. Steinbeck,et al.  Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. , 2006, Current pharmaceutical design.

[31]  J. Lindon,et al.  Pharmaco-metabonomic phenotyping and personalized drug treatment , 2006, Nature.

[32]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[33]  Sean R. Collins,et al.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.

[34]  John P. Overington,et al.  Can we rationally design promiscuous drugs? , 2006, Current opinion in structural biology.

[35]  Gavin Sherlock,et al.  Global analysis of gene function in yeast by quantitative phenotypic profiling , 2006, Molecular systems biology.

[36]  David S. Wishart,et al.  DrugBank: a comprehensive resource for in silico drug discovery and exploration , 2005, Nucleic Acids Res..

[37]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[38]  Peter D. Karp,et al.  MetaCyc: a multiorganism database of metabolic pathways and enzymes , 2005, Nucleic Acids Res..

[39]  A. Fliri,et al.  Analysis of drug-induced effect patterns to link structure and side effects of medicines , 2005, Nature chemical biology.

[40]  S. L. Wong,et al.  Towards a proteome-scale map of the human protein–protein interaction network , 2005, Nature.

[41]  Naryttza N. Diaz,et al.  The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.

[42]  H. Lehrach,et al.  A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome , 2005, Cell.

[43]  U. Bhalla,et al.  Systems modeling: a pathway to drug discovery. , 2005, Current opinion in chemical biology.

[44]  Robert P. St.Onge,et al.  Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents , 2005, PLoS genetics.

[45]  Ruili Huang,et al.  Linking tumor cell cytotoxicity to mechanism of drug action: An integrated analysis of gene expression, small‐molecule screening and structural databases , 2005, Proteins.

[46]  Daniel C. Liebler,et al.  Elucidating mechanisms of drug-induced toxicity , 2005, Nature Reviews Drug Discovery.

[47]  R. Russell,et al.  Illuminating drug discovery with biological pathways , 2005, FEBS letters.

[48]  L. Wodicka,et al.  A small molecule–kinase interaction map for clinical kinase inhibitors , 2005, Nature Biotechnology.

[49]  J. A. Grant,et al.  A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. , 2005, Journal of medicinal chemistry.

[50]  Catherine Brooksbank,et al.  The European Bioinformatics Institute's data resources: towards systems biology , 2004, Nucleic Acids Res..

[51]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..

[52]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[53]  Xiaoyang Xia,et al.  Classification of kinase inhibitors using a Bayesian model. , 2004, Journal of medicinal chemistry.

[54]  P. Demoly,et al.  Classification and epidemiology of hypersensitivity drug reactions. , 2004, Immunology and allergy clinics of North America.

[55]  Martin Thimm,et al.  Comparison of 2D Similarity and 3D Superposition. Application to Searching a Conformational Drug Database , 2004, J. Chem. Inf. Model..

[56]  Arun K. Ramani,et al.  Protein interaction networks from yeast to human. , 2004, Current opinion in structural biology.

[57]  Stuart L Schreiber,et al.  Chemical suppression of a genetic mutation in a zebrafish model of aortic coarctation , 2004, Nature Biotechnology.

[58]  James F Blake,et al.  Structure-based generation of viable leads from small combinatorial libraries. , 2004, Current opinion in drug discovery & development.

[59]  Gary D Bader,et al.  Global Mapping of the Yeast Genetic Interaction Network , 2004, Science.

[60]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[61]  J. C. Hinshaw,et al.  Discovering Modes of Action for Therapeutic Compounds Using a Genome-Wide Screen of Yeast Heterozygotes , 2004, Cell.

[62]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[63]  Leonard I. Zon,et al.  Cancer genetics and drug discovery in the zebrafish , 2003, Nature Reviews Cancer.

[64]  Pierre Acklin,et al.  Similarity Metrics for Ligands Reflecting the Similarity of the Target Proteins , 2003, J. Chem. Inf. Comput. Sci..

[65]  M. Tyers,et al.  The GRID: The General Repository for Interaction Datasets , 2003, Genome Biology.

[66]  Egon L. Willighagen,et al.  The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo-and Bioinformatics , 2003, J. Chem. Inf. Comput. Sci..

[67]  Bryan L. Roth,et al.  Salvinorin A: A potent naturally occurring nonnitrogenous κ opioid selective agonist , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Y. Martin,et al.  Do structurally similar molecules have similar biological activity? , 2002, Journal of medicinal chemistry.

[69]  J. Irwin,et al.  Lead discovery using molecular docking. , 2002, Current opinion in chemical biology.

[70]  P. Bork,et al.  Association of genes to genetically inherited diseases using data mining , 2002, Nature Genetics.

[71]  Gabriele Ausiello,et al.  MINT: the Molecular INTeraction database , 2006, Nucleic Acids Res..

[72]  John B. O. Mitchell.  The Relationship between the Sequence Identities of Alpha Helical Proteins in the PDB and the Molecular Similarities of Their Ligands , 2001, J. Chem. Inf. Comput. Sci..

[73]  R G Ulrich,et al.  Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. , 2001, Toxicology and applied pharmacology.

[74]  Torbjørn Rognes,et al.  Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors , 2000, Bioinform..

[75]  B. Roth,et al.  The Multiplicity of Serotonin Receptors: Uselessly Diverse Molecules or an Embarrassment of Riches? , 2000 .

[76]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[77]  Christian Lemmen,et al.  Computational methods for the structural alignment of molecules , 2000, J. Comput. Aided Mol. Des..

[78]  John M. Barnard,et al.  Chemical Similarity Searching , 1998, J. Chem. Inf. Comput. Sci..

[79]  H. Matter,et al.  Selecting optimally diverse compounds from structure databases: a validation study of two-dimensional and three-dimensional molecular descriptors. , 1997, Journal of medicinal chemistry.

[80]  G. S. Johnson,et al.  An Information-Intensive Approach to the Molecular Pharmacology of Cancer , 1997, Science.

[81]  R. Woosley,et al.  Changes in the pharmacokinetics and electrocardiographic pharmacodynamics of terfenadine with concomitant administration of erythromycin , 1992, Clinical pharmacology and therapeutics.

[82]  L. Zon,et al.  In vivo drug discovery in the zebrafish , 2005, Nature Reviews Drug Discovery.

[83]  Brian K. Shoichet,et al.  ZINC - A Free Database of Commercially Available Compounds for Virtual Screening , 2005, J. Chem. Inf. Model..

[84]  J. Waring,et al.  Idiosyncratic toxicity: mechanistic insights gained from analysis of prior compounds. , 2005, Current opinion in drug discovery & development.

[85]  T. Baillie,et al.  Drug-protein adducts: an industry perspective on minimizing the potential for drug bioactivation in drug discovery and development. , 2004, Chemical research in toxicology.

[86]  A. Sands,et al.  Knockouts model the 100 best-selling drugs—will they model the next 100? , 2003, Nature Reviews Drug Discovery.

[87]  X. Chen,et al.  TTD: Therapeutic Target Database , 2002, Nucleic Acids Res..

[88]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[89]  Paul Ernsberger,et al.  Salvinorin A: a potent naturally occurring nonnitrogenous kappa opioid selective agonist. , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[90]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..