Published in J Chem Inf Comput Sci on March 25, 2003
BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res (2004) 8.21
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics (2010) 5.77
The Blue Obelisk-interoperability in chemical informatics. J Chem Inf Model (2006) 4.88
Virtual computational chemistry laboratory--design and description. J Comput Aided Mol Des (2005) 3.83
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics (2010) 2.94
ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr. J Comput Aided Mol Des (2009) 2.76
In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics (2010) 2.61
OSCAR4: a flexible architecture for chemical text-mining. J Cheminform (2011) 2.44
VEGA--an open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. J Comput Aided Mol Des (2004) 2.41
STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res (2013) 2.32
Detection of IUPAC and IUPAC-like chemical names. Bioinformatics (2008) 2.26
Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinformatics (2007) 1.97
Small Molecule Subgraph Detector (SMSD) toolkit. J Cheminform (2009) 1.94
Collaborative development of predictive toxicology applications. J Cheminform (2010) 1.91
OrChem - An open source chemistry search engine for Oracle(R). J Cheminform (2009) 1.71
CDK-Taverna: an open workflow environment for cheminformatics. BMC Bioinformatics (2010) 1.68
HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC Genomics (2009) 1.61
The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age. J Cheminform (2011) 1.44
canSAR: an integrated cancer public translational research and drug discovery resource. Nucleic Acids Res (2011) 1.41
CHARMMing: a new, flexible web portal for CHARMM. J Chem Inf Model (2008) 1.38
Systematic identification of proteins that elicit drug side effects. Mol Syst Biol (2013) 1.28
New developments on the cheminformatics open workflow environment CDK-Taverna. J Cheminform (2011) 1.27
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Mol Syst Biol (2013) 1.22
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. J Cheminform (2011) 1.22
Natural product-likeness score revisited: an open-source, open-data implementation. BMC Bioinformatics (2012) 1.19
PROCOGNATE: a cognate ligand domain mapping for enzymes. Nucleic Acids Res (2007) 1.18
Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM). Nucleic Acids Res (2015) 1.17
SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism. ACS Med Chem Lett (2010) 1.17
Chemical predictive modelling to improve compound quality. Nat Rev Drug Discov (2013) 1.13
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. BMC Bioinformatics (2009) 1.13
CASMI: And the Winner is . . . Metabolites (2013) 1.12
BALL--biochemical algorithms library 1.3. BMC Bioinformatics (2010) 1.12
Towards interoperable and reproducible QSAR analyses: Exchange of datasets. J Cheminform (2010) 1.11
Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci U S A (2015) 1.10
Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration. J Cheminform (2011) 1.09
Optimal assignment methods for ligand-based virtual screening. J Cheminform (2009) 1.03
Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics. BMC Bioinformatics (2011) 1.03
Linking the Resource Description Framework to cheminformatics and proteochemometrics. J Biomed Semantics (2011) 1.01
LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. PLoS One (2013) 1.00
KNIME-CDK: Workflow-driven cheminformatics. BMC Bioinformatics (2013) 0.99
SwissBioisostere: a database of molecular replacements for ligand design. Nucleic Acids Res (2012) 0.98
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol (2008) 0.98
jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints. J Cheminform (2011) 0.98
ScafBank: a public comprehensive Scaffold database to support molecular hopping. Acta Pharmacol Sin (2009) 0.97
An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products. Nat Commun (2015) 0.96
Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network. Nat Commun (2014) 0.95
Enhanced ranking of PknB Inhibitors using data fusion methods. J Cheminform (2013) 0.95
Standardized drug and pharmacological class network construction. Stud Health Technol Inform (2013) 0.94
ChEMBL web services: streamlining access to drug discovery data and utilities. Nucleic Acids Res (2015) 0.94
MolFind: a software package enabling HPLC/MS-based identification of unknown chemical structures. Anal Chem (2012) 0.93
OMG: Open Molecule Generator. J Cheminform (2012) 0.93
The influence of negative training set size on machine learning-based virtual screening. J Cheminform (2014) 0.92
An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds. BMC Bioinformatics (2012) 0.92
Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse. BMC Bioinformatics (2010) 0.92
AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment. J Cheminform (2011) 0.92
Interpreting linear support vector machine models with heat map molecule coloring. J Cheminform (2011) 0.91
Tuning HERG out: antitarget QSAR models for drug development. Curr Top Med Chem (2014) 0.91
Bioclipse-R: integrating management and visualization of life science data with statistical analysis. Bioinformatics (2012) 0.91
The influence of the inactives subset generation on the performance of machine learning methods. J Cheminform (2013) 0.91
Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining. Proc Natl Acad Sci U S A (2016) 0.91
Development of dimethyl sulfoxide solubility models using 163,000 molecules: using a domain applicability metric to select more reliable predictions. J Chem Inf Model (2013) 0.90
An analysis of a 'community-driven' reconstruction of the human metabolic network. Metabolomics (2013) 0.90
Fragmentation trees for the structural characterisation of metabolites. Rapid Commun Mass Spectrom (2012) 0.90
Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets. Bioinformatics (2013) 0.90
Global analysis of publicly available safety data for 9,801 substances registered under REACH from 2008-2014. ALTEX (2016) 0.90
Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. Nucleic Acids Res (2013) 0.89
Tackling CASMI 2012: Solutions from MetFrag and MetFusion. Metabolites (2013) 0.89
A constructive approach for discovering new drug leads: Using a kernel methodology for the inverse-QSAR problem. J Cheminform (2009) 0.89
Ligand-Based Site of Metabolism Prediction for Cytochrome P450 2D6. ACS Med Chem Lett (2011) 0.89
Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol (2015) 0.88
Predicting retention time in hydrophilic interaction liquid chromatography mass spectrometry and its use for peak annotation in metabolomics. Metabolomics (2014) 0.87
Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction. BMC Bioinformatics (2008) 0.87
Feature combination networks for the interpretation of statistical machine learning models: application to Ames mutagenicity. J Cheminform (2014) 0.87
Determination of Abraham model solute descriptors for the monomeric and dimeric forms of trans-cinnamic acid using measured solubilities from the Open Notebook Science Challenge. Chem Cent J (2015) 0.87
QSAR DataBank - an approach for the digital organization and archiving of QSAR model information. J Cheminform (2014) 0.87
DemQSAR: predicting human volume of distribution and clearance of drugs. J Comput Aided Mol Des (2011) 0.86
A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs. Metabolomics (2014) 0.86
Metingear: a development environment for annotating genome-scale metabolic models. Bioinformatics (2013) 0.86
Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule. BMC Pharmacol (2010) 0.86
ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. BMC Bioinformatics (2015) 0.86
RMol: a toolset for transforming SD/Molfile structure information into R objects. Source Code Biol Med (2012) 0.86
Machine learning models identify molecules active against the Ebola virus in vitro. F1000Res (2015) 0.85
Self-organizing ontology of biochemically relevant small molecules. BMC Bioinformatics (2012) 0.85
OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data. BMC Bioinformatics (2010) 0.84
How accurately can we predict the melting points of drug-like compounds? J Chem Inf Model (2014) 0.84
MolClass: a web portal to interrogate diverse small molecule screen datasets with different computational models. Bioinformatics (2012) 0.83
Classification of chemical compounds to support complex queries in a pathway database. Comp Funct Genomics (2004) 0.83
Exploring uncharted territories: predicting activity cliffs in structure-activity landscapes. J Chem Inf Model (2012) 0.83
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. J Cheminform (2015) 0.82
MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J Cheminform (2016) 0.82
Toxicokinetic Triage for Environmental Chemicals. Toxicol Sci (2015) 0.82
Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach. Bioinformatics (2014) 0.81
DOGS: reaction-driven de novo design of bioactive compounds. PLoS Comput Biol (2012) 0.81
Modeling the Biodegradability of Chemical Compounds Using the Online CHEmical Modeling Environment (OCHEM). Mol Inform (2013) 0.80
Efficient ring perception for the Chemistry Development Kit. J Cheminform (2014) 0.80
Network-analysis-guided synthesis of weisaconitine D and liljestrandinine. Nature (2015) 0.80
Asymmetric clustering index in a case study of 5-HT1A receptor ligands. PLoS One (2014) 0.80
Analysis of public oral toxicity data from REACH registrations 2008-2014. ALTEX (2016) 0.80
A tree-based method for the rapid screening of chemical fingerprints. Algorithms Mol Biol (2010) 0.80
Analysis of Draize eye irritation testing and its prediction by mining publicly available 2008-2014 REACH data. ALTEX (2016) 0.79
Structural determination of paraffin boiling points. J Am Chem Soc (1947) 10.27
JChem: Java applets and modules supporting chemical database handling from web browsers J Chem Inf Comput Sci (2000) 4.35
Chemical markup, XML and the World-Wide Web. 2. Information objects and the CMLDOM. J Chem Inf Comput Sci (2001) 3.56
SENECA: A platform-independent, distributed, and parallel system for computer-assisted structure elucidation in organic chemistry. J Chem Inf Comput Sci (2001) 2.92
Java classes for managing chemical information and solving generalized equilibrium problems. J Chem Inf Comput Sci (2002) 2.58
Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. Curr Pharm Des (2006) 7.05
NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database. Phytochemistry (2004) 2.40
Linked open drug data for pharmaceutical research and development. J Cheminform (2011) 2.37
Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinformatics (2007) 1.97
NMRShiftDB-constructing a free chemical information system with open-source components. J Chem Inf Comput Sci (2003) 1.77
Bioclipse 2: a scriptable integration platform for the life sciences. BMC Bioinformatics (2009) 1.69
The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PLoS One (2011) 1.52
The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports. Bioinformatics (2010) 1.51
Bioclipse-R: integrating management and visualization of life science data with statistical analysis. Bioinformatics (2012) 0.91
Effects of long-range electrostatic forces on simulated protein folding kinetics. J Comput Chem (2008) 0.89
Cavity cooling of free silicon nanoparticles in high vacuum. Nat Commun (2013) 0.88
Lumbar-load analysis of manual patient-handling activities for biomechanical overload prevention among healthcare workers. Ann Occup Hyg (2012) 0.88
Localization by site-directed mutagenesis of a galantamine binding site on α7 nicotinic acetylcholine receptor extracellular domain. J Recept Signal Transduct Res (2010) 0.84
Open source drug discovery with bioclipse. Curr Top Med Chem (2012) 0.82
Changing computational research. The challenges ahead. Source Code Biol Med (2012) 0.80
A survey of quantitative descriptions of molecular structure. Curr Top Med Chem (2012) 0.77
Time resolved structure analysis of growing beta-amyloid fibers. J Struct Biol (2007) 0.77
Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation. Int J Mol Sci (2009) 0.76
Erratum: A data-oriented approach to making new molecules as a student experiment: Artificial intelligence-enabling FAIR publication of NMR data for organic esters. Magn Reson Chem (2022) 0.75
ADRIS - The Adverse Drug Reactions Information Scheme. Clin Neuropharmacol (2004) 0.75
ADRIS--The Adverse Drug Reactions Information Scheme. Pharmacogenetics (2003) 0.75