A Cheminformatic Toolkit for Mining Biomedical Knowledge

KEGG: Kyoto Encyclopedia of Genes and Genomes

1999 • 30,001 citations

KEGG: Kyoto Encyclopedia of Genes and Genomes

2000 • 26,574 citations

DrugBank: a comprehensive resource for in silico drug discovery and exploration

2005 • 3,635 citations

Mass spectrometry‐based metabolomics

2006 • 2,042 citations

Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program.

2001 • 1,979 citations

A gene expression database for the molecular pharmacology of cancer

2000 • 1,447 citations

The KEGG databases at GenomeNet

2002 • 1,444 citations

An Information-Intensive Approach to the Molecular Pharmacology of Cancer

1997 • 1,177 citations

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

2006 • 1,104 citations

The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics

2003 • 996 citations

IntAct: an open source molecular interaction database

2003 • 981 citations

The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures

2004 • 909 citations

The NIH Roadmap

2003 • 899 citations

Similarity-based virtual screening using 2D fingerprints

2006 • 801 citations

Chemosensitivity prediction by transcriptional profiling

2001 • 673 citations

Rational selection of training and test sets for the development of validated QSAR models.

2003 • 654 citations

Multidimensional Drug Profiling By Automated Microscopy

2004 • 647 citations

Metabolomics: Current technologies and future trends

2006 • 561 citations

Mitochondrion as a Novel Target of Anticancer Chemotherapy

2000 • 536 citations

Delocalized lipophilic cations selectively target the mitochondria of carcinoma cells

2001 • 523 citations

Predicting drug sensitivity and resistance

2004 • 517 citations

Development of a Chemical Structure Comparison Method for Integrated Analysis of Chemical and Genomic Information in the Metabolic Pathways

2003 • 465 citations

Exploring biology with small organic molecules

2004 • 459 citations

Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics

2006 • 442 citations

EDGAR: Extraction of Drugs, Genes And Relations from the Biomedical Literature

1999 • 428 citations

Plant metabolomics: towards biological function and mechanism

2006 • 419 citations

USING GRAPHICAL MODELS AND GENOMIC EXPRESSION DATA TO STATISTICALLY VALIDATE MODELS OF GENETIC REGULATORY NETWORKS

2000 • 394 citations

An informatics approach identifying markers of chemosensitivity in human cancer cell lines.

2000 • 394 citations

The Blue Obelisk—Interoperability in Chemical Informatics

2006 • 388 citations

Perturbational profiling of a cell-line model of tumorigenesis by using metabolic measurements

2005 • 356 citations

Chemography: The Art of Navigating in Chemical Space

2001 • 344 citations

A high-throughput cell migration assay using scratch wound healing, a comparison of image-based readout methods

2004 • 343 citations

Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule

2001 • 338 citations

Estimation of permeability by passive diffusion through Caco-2 cell monolayers using the drugs' lipophilicity and molecular weight

1998 • 336 citations

Prediction of intestinal permeability

2002 • 316 citations

LIGAND: database of chemical compounds and reactions in biological pathways

2002 • 300 citations

ESTIMATION OF GENETIC NETWORKS AND FUNCTIONAL STRUCTURES BETWEEN GENES BY USING BAYESIAN NETWORKS AND NONPARAMETRIC REGRESSION

2001 • 297 citations

Plant uptake and transport models for neutral and ionic chemicals

2004 • 296 citations

High content screening applied to large-scale cell biology

2003 • 286 citations

Membrane Transporters and Channels

2004 • 277 citations

Synthesis and application of functionally diverse 2,6,9-trisubstituted purine libraries as CDK inhibitors

1999 • 267 citations

Mining the Biomedical Literature in the Genomic Era: An Overview

2003 • 265 citations

ADME evaluation in drug discovery

2002 • 259 citations

HT29-MTX/Caco-2 Cocultures as an in Vitro Model for the Intestinal Epithelium: In Vitro–in Vivo Correlation with Permeability Data from Rats and Humans

1996 • 258 citations

Pathway Mapping Tools for Analysis of High Content Data

2006 • 257 citations

SAGA: a subgraph matching tool for biological graphs

2006 • 246 citations

Selective toxicity of rhodamine 123 in carcinoma cells in vitro.

1983 • 235 citations

A novel mitochondriotoxic small molecule that selectively inhibits tumor cell growth

2002 • 224 citations

An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes

2004 • 221 citations

Associating Genes with Gene Ontology Codes Using a Maximum Entropy Analysis of Biomedical Literature

2002 • 203 citations

Myoseverin, a microtubule-binding molecule with novel cellular effects

2000 • 200 citations

RNA-Selective, Live Cell Imaging Probes for Studying Nuclear Structure and Function

2006 • 199 citations

sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank

2006 • 191 citations

An efficient rapid system for profiling the cellular activities of molecular libraries

2006 • 186 citations

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

2006 • 186 citations

ADME Evaluation in Drug Discovery. 5. Correlation of Caco-2 Permeation with Simple Molecular Properties

2004 • 185 citations

Advances in High Content Screening for Drug Discovery

2003 • 184 citations

A predictive model for the selective accumulation of chemicals in tumor cells

2005 • 178 citations

In Silico Prediction of Membrane Permeability from Calculated Molecular Parameters

2005 • 174 citations

Drug permeation in biomembranes

2004 • 173 citations

Effect of molecular charge on intestinal epithelial drug transport: pH-dependent transport of cationic drugs.

1999 • 172 citations

Genomics and natural language processing

2002 • 167 citations

Toxicokinetic modeling and its applications in chemical risk assessment

2003 • 165 citations

Functional Role of P-Glycoprotein in Limiting Intestinal Absorption of Drugs: Contribution of Passive Permeability to P-Glycoprotein Mediated Efflux Transport

2004 • 152 citations

COMBINING MICROARRAYS AND BIOLOGICAL KNOWLEDGE FOR ESTIMATING GENE NETWORKS VIA BAYESIAN NETWORKS

2004 • 151 citations

Searching Techniques for Databases of Two- and Three-Dimensional Chemical Structures

2005 • 149 citations

Mitochondrial Expression of the Human Equilibrative Nucleoside Transporter 1 (hENT1) Results in Enhanced Mitochondrial Toxicity of Antiviral Drugs

2004 • 144 citations

Developmental Therapeutics Program at the NCI: molecular target and drug discovery process

2002 • 143 citations

QSAR Modeling of Human Serum Protein Binding with Several Modeling Techniques Utilizing Structure−Information Representation

2006 • 143 citations

Analyzing Cellular Biochemistry in Terms of Molecular Networks

2004 • 141 citations

Panel of human cancer cell lines provides valuable database for drug discovery and bioinformatics

2003 • 141 citations

Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand–protein inverse docking approach

2001 • 141 citations

Screening for Cell Migration Inhibitors via Automated Microscopy Reveals a Rho-Kinase Inhibitor

2005 • 139 citations

Combinatorial QSAR Modeling of P-Glycoprotein Substrates

2006 • 134 citations

Bayesian analysis of signaling networks governing embryonic stem cell fate decisions

2004 • 131 citations

Molecular Similarity Measures

2010 • 130 citations

Relationship of Stereochemical and Skeletal Diversity of Small Molecules to Cellular Measurement Space

2004 • 130 citations

Bayesian Network Approach to Cell Signaling Pathway Modeling

2002 • 124 citations

A Novel Microtubule Destabilizing Entity from Orthogonal Synthesis of Triazine Library and Zebrafish Embryo Screening

2002 • 123 citations

MPW: the Metabolic Pathways Database

1998 • 123 citations

A Small‐Molecule Agonist of the Wnt Signaling Pathway

2005 • 123 citations

Text-based discovery in biomedicine: the architecture of the DAD-system.

2000 • 122 citations

Similarity-based approaches to virtual screening

2003 • 120 citations

Phenotypic Screening of Small Molecule Libraries by High Throughput Cell Imaging

2003 • 118 citations

Predicting the behaviour and selectivity of fluorescent probes for lysosomes and related structures by means of structure-activity models

1991 • 115 citations

Extracting molecular binding relationships from biomedical text

2000 • 115 citations

Structural analysis of expanding metabolic networks.

2004 • 112 citations

Development of predictive pharmacokinetic simulation models for drug discovery

2000 • 112 citations

Prediction of the oral absorption of low-permeability drugs using small intestine-like 2/4/A1 cell monolayers.

2003 • 111 citations

Passive permeation of organic compounds through biological tissue: a non-steady-state theory.

1969 • 111 citations

Chemoinformatics – similarity and diversity in chemical libraries

2000 • 110 citations

Recovering the true targets of specific ligands by virtual screening of the protein data bank

2004 • 110 citations

A Synthetic Small Molecule That Induces Neuronal Differentiation of Adult Hippocampal Neural Progenitor Cells

2005 • 104 citations

Small‐Molecule Screening and Profiling by Using Automated Microscopy

2004 • 102 citations

Application of Validated QSAR Models of D₁Dopaminergic Antagonists for Database Mining

2005 • 97 citations

Interpreting Computational Neural Network QSAR Models: A Measure of Descriptor Importance

2005 • 96 citations

Interaction of molecular probes with living cells and tissues. Part 2

1990 • 93 citations

Separate Roles for the Golgi Apparatus and Lysosomes in the Sequestration of Drugs in the Multidrug-resistant Human Leukemic Cell Line HL-60

2003 • 91 citations

Kekule: OCR-optical chemical (structure) recognition

1992 • 90 citations

Determining the Validity of a QSAR Model − A Classification Approach

2004 • 89 citations

Nucleoside transporters in the disposition and targeting of nucleoside analogs in the kidney

2003 • 84 citations

Mining molecular binding terminology from biomedical text.

1999 • 84 citations

Similarity Searching in Files of Three-Dimensional Chemical Structures: Analysis of the BIOSTER Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors

1999 • 83 citations

Predicting Protein−Ligand Binding Affinities Using Novel Geometrical Descriptors and Machine-Learning Methods

2004 • 82 citations

A Pharmacophore Hypothesis for P-Glycoprotein Substrate Recognition Using GRIND-Based 3D-QSAR

2005 • 82 citations

Predictive models for hERG potassium channel blockers

2005 • 82 citations

Efficient RMSD measures for the comparison of two molecular ensembles

2002 • 81 citations

Evaluation of Selected Chemotypes in Coupled Cellular and Molecular Target-Based Screens Identifies Novel HIV-1 Zinc Finger Inhibitors

1996 • 80 citations

Pharmacokinetically Based Mapping Device for Chemical Space Navigation

2002 • 78 citations

Mitochondrial ABC transporters

2001 • 76 citations

A knowledge model for analysis and simulation of regulatory networks

2000 • 76 citations

Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions

2006 • 75 citations

F16, a Mitochondriotoxic Compound, Triggers Apoptosis or Necrosis Depending on the Genetic Background of the Target Carcinoma Cell

2004 • 74 citations

Inhibition and Reversal of Myogenic Differentiation by Purine-Based Microtubule Assembly Inhibitors

2002 • 73 citations

Chemical literature data extraction: The CLiDE Project

1993 • 72 citations

Exploring text mining from MEDLINE.

2002 • 68 citations

Alignment of three-dimensional molecules using an image recognition algorithm

2004 • 67 citations

Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures

2000 • 66 citations

MeSHmap: a text mining tool for MEDLINE.

2001 • 66 citations

Why fluorescent probes for endoplasmic reticulum are selective: an experimental and QSAR-modelling study

2003 • 66 citations

A cyclin-dependent kinase inhibitor inducing cancer cell differentiation: Biochemical identification using Xenopus egg extracts

1999 • 65 citations

Dissection of Melanogenesis with Small Molecules Identifies Prohibitin as a Regulator

2005 • 65 citations

ADVANCES IN CHEMICAL GENETICS

2005 • 64 citations

Comparison of chemical clustering methods using graph- and fingerprint-based similarity measures

2003 • 62 citations

Prediction of Caco-2 cell permeability using a combination of MO-calculation and neural network

2002 • 61 citations

Past, Present, and Future of High Content Screening and the Field of Cellomics

2006 • 61 citations

LIGAND: chemical database of enzyme reactions

2000 • 60 citations

Exploring protein–ligand recognition with Binding MOAD

2005 • 60 citations

Generation of QSAR sets with a self-organizing map

2004 • 58 citations

Chemical information management in drug discovery: optimizing the computational and combinatorial chemistry interfaces11Color Plates for this article are on page 541.

2000 • 57 citations

PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures

2004 • 57 citations

Exploring the chemogenomic knowledge space with annotated chemical libraries

2004 • 55 citations

Novel Phosphonium Salts Displayin Vitroandin VivoCytotoxic Activity against Human Ovarian Cancer Cell Lines

1996 • 54 citations

A General Approach for the Prediction of the Intestinal Absorption of Drugs: Regression Analysis Using the Physicochemical Properties and Drug–Membrane Electrostatic Interaction

1998 • 54 citations

Fast drug-receptor mapping by site-directed distances: a novel method of predicting new pharmacological leads

1991 • 52 citations

A new topological descriptors based model for predicting intestinal epithelial transport of drugs in Caco-2 cell culture.

2004 • 52 citations

Structure‐staining relationships in histochemistry and biological staining

1980 • 51 citations

Accumulation of fluorescent non‐cationic probes in mitochondria of cultured cells: observations, a proposed mechanism, and some implications

1991 • 51 citations

High-Content Screening and Profiling of Drug Activity in an Automated Centrosome-Duplication Assay

2004 • 50 citations

dbtop: Topomer similarity searching of conventional structure databases

2002 • 50 citations

Using the National Cancer Institute Anticancer Drug Screen to Assess the Effect ofMRPExpression on Drug Sensitivity Profiles

1998 • 50 citations

Identification of Compounds that Bind Mitochondrial F1F0 ATPase by Screening a Triazine Library for Correction of Albinism

2004 • 50 citations

Enabling the exploration of biochemical pathways

2004 • 50 citations

Establishing connections between microarray expression data and chemotherapeutic cancer pharmacology.

2002 • 50 citations

Synthesis and Evaluation of Novel Rhodacyanine Dyes That Exhibit Antitumor Activity

1997 • 49 citations

Similarity searching in databases of three-dimensional molecules and macromolecules

1992 • 49 citations

Of truth and pathways: chasing bits of information through myriads of articles

2002 • 49 citations

Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI)

2006 • 49 citations

Suitability of Molecular Descriptors for Database Mining. A Comparative Analysis

2002 • 48 citations

Identification of the F1F0 mitochondrial ATPase as a target for modulating skin pigmentation by screening a tagged triazine library in zebrafish

2005 • 47 citations

Integromic Analysis of the NCI-60 Cancer Cell Lines

2004 • 46 citations

Requirements, Features, and Performance of High Content Screening Platforms

2006 • 46 citations

Optical recognition of chemical graphics

2002 • 46 citations

Using genome-wide transcriptional profiling to elucidate small-molecule mechanism

2004 • 46 citations

New developments in PEST shape/property hybrid descriptors.

2003 • 44 citations

Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure.

2000 • 44 citations

A Cell-Based Molecular Transport Simulator for Pharmacokinetic Prediction and Cheminformatic Exploration

2006 • 44 citations

Molecular Similarity Measures

2004 • 44 citations

Comprehensive analysis of pathway or functionally related gene expression in the National Cancer Institute's anticancer screen

2006 • 43 citations

Linking pathway gene expressions to the growth inhibition response from the National Cancer Institute's anticancer screen and drug mechanism of action

2005 • 41 citations

Linking tumor cell cytotoxicity to mechanism of drug action: An integrated analysis of gene expression, small-molecule screening and structural databases

2005 • 40 citations

Structure‐staining relationships in histochemistry and biological staining

1980 • 39 citations

Synthesis and Biological Evaluation of Myoseverin Derivatives: Microtubule Assembly Inhibitors

2001 • 39 citations

The completed human genome: implications for chemical biology

2003 • 38 citations

The Role of the VPS4A-Exosome Pathway in the Intrinsic Egress Route of a DNA-Binding Anticancer Drug

2006 • 38 citations

Discrimination techniques applied to the NCI in vitro anti‐tumour drug screen: Predicting biochemical mechanism of action

1994 • 38 citations

Interactions of molecular probes with living cells and tissues. Part 1. Some general mechanistic proposals, making use of a simplistic Chinese box model

1990 • 37 citations

A Cell Fractionation Approach for the Quantitative Analysis of Subcellular Drug Disposition

2004 • 36 citations

Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction

2004 • 36 citations

Modeling the benzodiazepine receptor binding site by the general three-dimensional structure-directed quantitative structure-activity relationship method REMOTEDISC.

1990 • 35 citations

Simulation of infrared spectra: an infrared spectral simulation program (SIRS) which uses DARC topological substructures

1990 • 34 citations

Linking the growth inhibition response from the National Cancer Institute's anticancer screen to gene expression levels and other molecular target data

2003 • 32 citations

Supertargeted Chemistry: Identifying Relationships Between Molecular Structures and their Sub-Cellular Distribution

2003 • 31 citations

Hierarchical PLS Modeling for Predicting the Binding of a Comprehensive Set of Structurally Diverse Protein−Ligand Complexes

2006 • 30 citations

Chemoinformatic Analysis of a Supertargeted Combinatorial Library of Styryl Molecules

2003 • 30 citations

Automatic generation of alignments for 3D QSAR analyses

2001 • 28 citations

Fragmental Methods in the Analysis of Biological Activities of Diverse Compound Sets

2003 • 28 citations

Computational perception and recognition of digitized molecular structures

1990 • 27 citations

C-QSAR: a database of 18,000 QSARs and associated biological and physical data.

2003 • 27 citations

Using High-Throughput Screening Data To Discriminate Compounds with Single-Target Effects from Those with Side Effects

2006 • 26 citations

Rational Principles of Compound Selection for Combinatorial Library Design

2002 • 26 citations

Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries.

2002 • 24 citations

Challenges for chemoinformatics education in drug discovery

2006 • 24 citations

Peer Reviewed: Extracting Information From the Literature By Text Mining

2001 • 22 citations

Diversity and Coverage of Structural Sublibraries Selected Using the SAGE and SCA Algorithms

2001 • 21 citations

Evaluating Chemical Structure Similarity as an Indicator of Cellular Growth Inhibition

2005 • 20 citations

KNOWLEDGE REPRESENTATION AND INDEXING USING THE UNIFIED MEDICAL LANGUAGE SYSTEM

1999 • 19 citations

The Great Multidrug-Resistance Paradox

2006 • 17 citations

System Dynamics of Subcellular Transport

2004 • 17 citations

Fragment analysis in small molecule discovery.

2002 • 15 citations

Exploratory data analytic techniques to evaluate anticancer agents screened in a cell culture panel

1992 • 15 citations

Chemical Information Based Scaling of Molecular Descriptors: A Universal Chemical Scale for Library Design and Analysis

2002 • 14 citations

Videoconferencing and Other Distance Education Techniques in Chemoinformatics Teaching and Research at Indiana University

2006 • 13 citations

Overview of Informatics for High Content Screening

2006 • 13 citations

A rational approach to personalized anticancer therapy: chemoinformatic analysis reveals mechanistic gene-drug associations.

2003 • 11 citations

The measurement of molecular diversity by receptor site interaction simulation.

1998 • 11 citations

SYMBOLIC INFERENCE OF XENOBIOTIC METABOLISM

2003 • 10 citations

Chemical Genomics

2004 • 9 citations

Augmenting Connectivity Information by Compound Name Parsing: Automatic Assignment of Stereochemistry and Isotope Labeling

1995 • 9 citations

Query Generation to Search for Inhibitors of Enzymatic Reactions

2006 • 9 citations

Deducing molecular similarity using Voronoi binding sites

1993 • 7 citations

A guest molecule–host cavity fitting algorithm to mine PDB for small molecule targets

2006 • 5 citations

Prediction of Caco-2 cell permeability using partial least squares multivariate analysis.

2001 • 5 citations

Exploratory Chemoinformatic Analysis of Cell Type-Selective Anticancer Drug Targeting

2004 • 3 citations

Voronoi receptor site models.

1989 • 3 citations

JChemTidy: A Tool for Converting Chemical Web Document Collections to an XHTML Representation

2001 • 3 citations

Beyond the hyperactive molecule: search, salvage and visualization of chemical information from the Internet.

1996 • 2 citations

Deleted Work

1955 • 0 citations