A cheminformatic toolkit for mining biomedical knowledge (Q36769973)

16 August 2017

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title

A cheminformatic toolkit for mining biomedical knowledge (English)

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16 August 2017

Gus R Rosania

1

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16 August 2017

Gordon Crippen

2

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16 August 2017

Peter Woolf

3

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16 August 2017

David States

4

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16 August 2017

Kerby Shedden

5

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16 August 2017

24 March 2007

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16 August 2017

Pharmaceutical Research

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16 August 2017

24

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16 August 2017

10

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16 August 2017

1791-1802

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Rational principles of compound selection for combinatorial library design

16 August 2017

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https://api.crossref.org/works/10.1007%2FS11095-007-9285-5

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

21 January 2018

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https://api.crossref.org/works/10.1007%2FS11095-007-9285-5

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

21 January 2018

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https://api.crossref.org/works/10.1007%2FS11095-007-9285-5

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

21 January 2018

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https://api.crossref.org/works/10.1007%2FS11095-007-9285-5

Phenotypic screening of small molecule libraries by high throughput cell imaging

21 January 2018

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https://api.crossref.org/works/10.1007%2FS11095-007-9285-5

Kekule: OCR-optical chemical (structure) recognition

21 January 2018

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https://api.crossref.org/works/10.1007%2FS11095-007-9285-5

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

21 January 2018

1 reference

12 December 2020

A pharmacophore hypothesis for P-glycoprotein substrate recognition using GRIND-based 3D-QSAR.

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12 December 2020

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

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12 December 2020

Analyzing cellular biochemistry in terms of molecular networks

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12 December 2020

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

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12 December 2020

Chemoinformatics - similarity and diversity in chemical libraries

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12 December 2020

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

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12 December 2020

LIGAND: chemical database of enzyme reactions

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12 December 2020

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

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12 December 2020

Synthesis and evaluation of novel rhodacyanine dyes that exhibit antitumor activity

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12 December 2020

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

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12 December 2020

Query generation to search for inhibitors of enzymatic reactions.

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12 December 2020

High content screening applied to large-scale cell biology

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12 December 2020

KEGG: kyoto encyclopedia of genes and genomes

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12 December 2020

Plant uptake and transport models for neutral and ionic chemicals

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12 December 2020

Chemometric analysis of ligand receptor complementarity: identifying Complementary Ligands Based on Receptor Information (CoLiBRI).

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12 December 2020

Structure-staining relationships in histochemistry and biological staining. I. Theoretical background and a general account of correlation of histochemical staining with the chemical structure of the reagents used

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12 December 2020

Bayesian network approach to cell signaling pathway modeling

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12 December 2020

Mitochondrion as a novel target of anticancer chemotherapy

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12 December 2020

Molecular similarity measures

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12 December 2020

Enabling the exploration of biochemical pathways

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12 December 2020

F16, a mitochondriotoxic compound, triggers apoptosis or necrosis depending on the genetic background of the target carcinoma cell

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12 December 2020

Predicting drug sensitivity and resistance: profiling ABC transporter genes in cancer cells

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12 December 2020

Toxicokinetic modeling and its applications in chemical risk assessment

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12 December 2020

LIGAND: database of chemical compounds and reactions in biological pathways

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12 December 2020

Chemical information based scaling of molecular descriptors: a universal chemical scale for library design and analysis

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12 December 2020

The measurement of molecular diversity by receptor site interaction simulation

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12 December 2020

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

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12 December 2020

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

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12 December 2020

A general approach for the prediction of the intestinal absorption of drugs: regression analysis using the physicochemical properties and drug-membrane electrostatic interaction.

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12 December 2020

Exploring text mining from MEDLINE.

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12 December 2020

An information-intensive approach to the molecular pharmacology of cancer.

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12 December 2020

Advances in high content screening for drug discovery

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12 December 2020

Myoseverin, a microtubule-binding molecule with novel cellular effects

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12 December 2020

Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks

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12 December 2020

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

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12 December 2020

The great multidrug-resistance paradox

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12 December 2020

Small-molecule screening and profiling by using automated microscopy

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12 December 2020

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

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12 December 2020

Chemoinformatic analysis of a supertargeted combinatorial library of styryl molecules.

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12 December 2020

Genomics and natural language processing

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12 December 2020

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

1 reference

12 December 2020

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

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12 December 2020

Inhibition and reversal of myogenic differentiation by purine-based microtubule assembly inhibitors

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12 December 2020

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

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12 December 2020

Functional role of P-glycoprotein in limiting intestinal absorption of drugs: contribution of passive permeability to P-glycoprotein mediated efflux transport

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12 December 2020

A cell-based molecular transport simulator for pharmacokinetic prediction and cheminformatic exploration.

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12 December 2020

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

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12 December 2020

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

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12 December 2020

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

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12 December 2020

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12 December 2020

Plant metabolomics: towards biological function and mechanism

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12 December 2020

MeSHmap: a text mining tool for MEDLINE.

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12 December 2020

Voronoi receptor site models

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12 December 2020

Mitochondrial expression of the human equilibrative nucleoside transporter 1 (hENT1) results in enhanced mitochondrial toxicity of antiviral drugs.

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12 December 2020

Chemosensitivity prediction by transcriptional profiling

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12 December 2020

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

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12 December 2020

In silico prediction of membrane permeability from calculated molecular parameters.

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12 December 2020

An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes.

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12 December 2020

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

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12 December 2020

New developments in PEST shape/property hybrid descriptors.

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12 December 2020

The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures

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12 December 2020

Mining the biomedical literature in the genomic era: an overview

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12 December 2020

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

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12 December 2020

Prediction of intestinal permeability

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12 December 2020

Identification of compounds that bind mitochondrial F1F0 ATPase by screening a triazine library for correction of albinism

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12 December 2020

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

1 reference

12 December 2020

The Blue Obelisk-interoperability in chemical informatics

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12 December 2020

Combinatorial QSAR modeling of P-glycoprotein substrates

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12 December 2020

The KEGG databases at GenomeNet

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12 December 2020

Deducing molecular similarity using Voronoi binding sites

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12 December 2020

Application of validated QSAR models of D1 dopaminergic antagonists for database mining

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12 December 2020

QSAR modeling of human serum protein binding with several modeling techniques utilizing structure-information representation.

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12 December 2020

Membrane transporters and channels: role of the transportome in cancer chemosensitivity and chemoresistance

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12 December 2020

Fragment analysis in small molecule discovery

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12 December 2020

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

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12 December 2020

Synthesis and biological evaluation of myoseverin derivatives: microtubule assembly inhibitors.

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12 December 2020

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

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12 December 2020

Evaluating chemical structure similarity as an indicator of cellular growth inhibition

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12 December 2020

Determining the validity of a QSAR model--a classification approach.

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12 December 2020

Chemical information management in drug discovery: optimizing the computational and combinatorial chemistry interfaces.

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12 December 2020

Drug permeation in biomembranes: in vitro and in silico prediction and influence of physicochemical properties

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12 December 2020

Dissection of melanogenesis with small molecules identifies prohibitin as a regulator

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12 December 2020

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

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12 December 2020

Advances in chemical genetics

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12 December 2020

Integromic analysis of the NCI-60 cancer cell lines

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12 December 2020

Extracting information from the literature by text mining

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12 December 2020

Mining molecular binding terminology from biomedical text

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12 December 2020

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

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12 December 2020

A cell fractionation approach for the quantitative analysis of subcellular drug disposition

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12 December 2020

Predictive models for hERG potassium channel blockers

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12 December 2020

Metabolomics: current technologies and future trends.

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12 December 2020

Past, present, and future of high content screening and the field of cellomics

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12 December 2020

Selective toxicity of rhodamine 123 in carcinoma cells in vitro

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12 December 2020

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

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12 December 2020

Using high-throughput screening data to discriminate compounds with single-target effects from those with side effects

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12 December 2020

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

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12 December 2020

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

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12 December 2020

Diversity and coverage of structural sublibraries selected using the SAGE and SCA algorithms

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12 December 2020

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

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12 December 2020

Pathway mapping tools for analysis of high content data

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12 December 2020

Medicine. The NIH Roadmap

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12 December 2020

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12 December 2020

Exploring biology with small organic molecules

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12 December 2020

The role of the VPS4A-exosome pathway in the intrinsic egress route of a DNA-binding anticancer drug

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12 December 2020

IntAct: an open source molecular interaction database

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12 December 2020

MPW: the Metabolic Pathways Database

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12 December 2020

Establishing connections between microarray expression data and chemotherapeutic cancer pharmacology

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12 December 2020

Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.

1 reference

12 December 2020

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

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12 December 2020

Evaluation of selected chemotypes in coupled cellular and molecular target-based screens identifies novel HIV-1 zinc finger inhibitors

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12 December 2020

Symbolic inference of xenobiotic metabolism

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12 December 2020

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

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12 December 2020

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

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12 December 2020

EDGAR: extraction of drugs, genes and relations from the biomedical literature

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12 December 2020

Requirements, features, and performance of high content screening platforms

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12 December 2020

Using the national cancer institute anticancer drug screen to assess the effect of MRP expression on drug sensitivity profiles

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12 December 2020

SAGA: a subgraph matching tool for biological graphs

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12 December 2020

Exploratory chemoinformatic analysis of cell type-selective anticancer drug targeting

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12 December 2020

A gene expression database for the molecular pharmacology of cancer

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12 December 2020

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12 December 2020

Suitability of molecular descriptors for database mining. A comparative analysis.

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12 December 2020

High-content screening and profiling of drug activity in an automated centrosome-duplication assay

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12 December 2020

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

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12 December 2020

Structural analysis of expanding metabolic networks.

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12 December 2020

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

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12 December 2020

Mitochondria give cells a tan

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12 December 2020

Supertargeted chemistry: identifying relationships between molecular structures and their sub-cellular distribution

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12 December 2020

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

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12 December 2020

A small-molecule agonist of the Wnt signaling pathway

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12 December 2020

Bayesian analysis of signaling networks governing embryonic stem cell fate decisions.

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12 December 2020

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

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12 December 2020

Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods.

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12 December 2020

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

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12 December 2020

System dynamics of subcellular transport

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12 December 2020

A knowledge model for analysis and simulation of regulatory networks.

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12 December 2020

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

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12 December 2020

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

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12 December 2020

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

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12 December 2020

Knowledge representation and indexing using the unified medical language system

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12 December 2020

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

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12 December 2020

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12 December 2020

RNA-selective, live cell imaging probes for studying nuclear structure and function

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12 December 2020

Chemical genomics: probing protein function using small molecules

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12 December 2020

Challenges for chemoinformatics education in drug discovery

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12 December 2020

A novel mitochondriotoxic small molecule that selectively inhibits tumor cell growth.

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12 December 2020

Developmental therapeutics program at the NCI: molecular target and drug discovery process

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12 December 2020

A synthetic small molecule that induces neuronal differentiation of adult hippocampal neural progenitor cells

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12 December 2020

Diversity-oriented organic synthesis and proteomics. New frontiers for chemistry & biology

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12 December 2020

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

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12 December 2020

Combining microarrays and biological knowledge for estimating gene networks via bayesian networks

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12 December 2020

Dbtop: topomer similarity searching of conventional structure databases

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12 December 2020

Alignment of three-dimensional molecules using an image recognition algorithm

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12 December 2020

Multidimensional drug profiling by automated microscopy.

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12 December 2020

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

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12 December 2020

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

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12 December 2020

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

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12 December 2020

Pharmacokinetically based mapping device for chemical space navigation

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12 December 2020

Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression.

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12 December 2020

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

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12 December 2020

Development of predictive pharmacokinetic simulation models for drug discovery

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12 December 2020

ADME evaluation in drug discovery. 5. Correlation of Caco-2 permeation with simple molecular properties.

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12 December 2020

Overview of informatics for high content screening.

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12 December 2020

Searching techniques for databases of two- and three-dimensional chemical structures.

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12 December 2020

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

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12 December 2020

Automatic generation of alignments for 3D QSAR analyses

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12 December 2020

Exploring the chemogenomic knowledge space with annotated chemical libraries

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12 December 2020

Generation of QSAR sets with a self-organizing map.

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12 December 2020

Chemography: the art of navigating in chemical space.

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12 December 2020

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

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12 December 2020

Exploring protein-ligand recognition with Binding MOAD

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12 December 2020

Screening for cell migration inhibitors via automated microscopy reveals a Rho-kinase inhibitor

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12 December 2020

Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature

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12 December 2020

The completed human genome: implications for chemical biology

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12 December 2020

Interaction of molecular probes with living cells and tissues. Part 2. A structure-activity analysis of mitochondrial staining by cationic probes, and a discussion of the synergistic nature of image-based and biochemical approaches

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12 December 2020

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

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12 December 2020

Novel phosphonium salts display in vitro and in vivo cytotoxic activity against human ovarian cancer cell lines

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12 December 2020

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

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12 December 2020

sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank

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12 December 2020

Relationship of stereochemical and skeletal diversity of small molecules to cellular measurement space

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12 December 2020

Interpreting computational neural network QSAR models: a measure of descriptor importance.

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12 December 2020

Mass spectrometry-based metabolomics

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12 December 2020

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

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12 December 2020

Mitochondrial ABC transporters

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12 December 2020

Videoconferencing and other distance education techniques in chemoinformatics teaching and research at Indiana University

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12 December 2020

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

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12 December 2020

JChemTidy: a tool for converting chemical Web document collections to an XHTML representation.

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12 December 2020

A novel microtubule destabilizing entity from orthogonal synthesis of triazine library and zebrafish embryo screening

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12 December 2020

Efficient RMSD measures for the comparison of two molecular ensembles. Root-mean-square deviation

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12 December 2020

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

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12 December 2020

Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring functions

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12 December 2020

Delocalized lipophilic cations selectively target the mitochondria of carcinoma cells

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12 December 2020

10.1007/S11095-007-9285-5

Identifiers

DOI

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release_ehy6anegbraprmsje34qehiobm

16 August 2017

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Fatcat

https://api.fatcat.wiki/v0/release/ehy6anegbraprmsje34qehiobm

24 November 2022

mapped directly with Wikidata item

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