Articles
Page 22 of 30
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Citation: Journal of Cheminformatics 2013 5(Suppl 1):P53
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Building QSAR for HTS in vitro assays - a study for the prediction of Aryl hydrocarbon receptor activators
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P51 -
Using graph-based consensus clustering for combining K-means clustering of heterogeneous chemical structures
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P50 -
Finding unusual peptides on the internet using plain three letter sequence codes
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P49 -
Neural network based classification of acute toxicity of phthalate esters to fathead minnow
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P47 -
More than a rigid framework: molecular design using secondary structure element information
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P45 -
Chemogenomics approaches to rationalising compound action of traditional Chinese and Ayurvedic medicines
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P44 -
Expanding natural product chemistry resources at the EBI
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P43 -
Ligand-based and structure-based design of novel histone demethylase inhibitors
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P41 -
Optimising chemical information workflows: integrating Reaxys - use cases and applications
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P39 -
InChI - the worldwide chemical structure standard
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P37 -
Revised classification of kinases based on bioactivity data: the importance of data density and choice of visualization
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P24 -
Analysis of naphthoquinone derivatives as topoisomerase I inhibitors using fragment based QSAR
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P22 -
Taking the PubChem web sketcher to the next level
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P20 -
In silico target prediction: identification of on- and off-targets for crop protection agents
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P18 -
Using Pareto points for model identification in predictive toxicology
Predictive toxicology is concerned with the development of models that are able to predict the toxicity of chemicals. A reliable prediction of toxic effects of chemicals in living systems is highly desirable i...
Citation: Journal of Cheminformatics 2013 5:16 -
International chemical identifier for chemical reactions
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O16 -
Efficient mining of protein kinase structural data
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P16 -
Dataset overlap density analysis
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O14 -
Force-field-based minimizations of protein-ligand complexes in the blink of an eye
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P14 -
Nemesis - a molecular modeling package
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P12 -
Quantifying the shifts in physicochemical property space introduced by the metabolism of small organic molecules
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O12 -
Computational prediction of heterogeneous interface properties at the atomic level
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O10 -
Is the novel amyloid-β tetramer fold a stable conformation?
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P10 -
Stability of single and double layer fibrillar amyloid-β oligomers
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P9 -
Towards a complete structure of the hERG channel
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P7 -
Automatic docking of a small number of ligands into a large number of binding sites
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P5 -
Mining basic active structures from a large-scale database
The Pubchem Database is a large-scale resource for chemical information, containing millions of chemical compound activities derived by high-throughput screening (HTS). The ability to extract characteristic su...
Citation: Journal of Cheminformatics 2013 5:15 -
Applications of the InChI in cheminformatics with the CDK and Bioclipse
The InChI algorithms are written in C++ and not available as Java library. Integration into software written in Java therefore requires a bridge between C and Java libraries, provided by the Java Native Interf...
Citation: Journal of Cheminformatics 2013 5:14 -
TB Mobile: a mobile app for anti-tuberculosis molecules with known targets
An increasing number of researchers are focused on strategies for developing inhibitors of Mycobacterium tuberculosis (Mtb) as tuberculosis (TB) drugs.
Citation: Journal of Cheminformatics 2013 5:13 -
Computational mass spectrometry for small molecules
The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from...
Citation: Journal of Cheminformatics 2013 5:12 -
Dragon exploration system on marine sponge compounds interactions
Natural products are considered a rich source of new chemical structures that may lead to the therapeutic agents in all major disease areas. About 50% of the drugs introduced in the market in the last 20 years...
Citation: Journal of Cheminformatics 2013 5:11 -
InChI in the wild: an assessment of InChIKey searching in Google
While chemical databases can be queried using the InChI string and InChIKey (IK) the latter was designed for open-web searching. It is becoming increasingly effective for this since more sources enhance crawli...
Citation: Journal of Cheminformatics 2013 5:10 -
Random forests for feature selection in QSPR Models - an application for predicting standard enthalpy of formation of hydrocarbons
One of the main topics in the development of quantitative structure-property relationship (QSPR) predictive models is the identification of the subset of variables that represent the structure of a molecule an...
Citation: Journal of Cheminformatics 2013 5:9 -
New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms
Solvation free energy is a fundamental thermodynamic quantity that should be determined to estimate various physicochemical properties of a molecule and the desolvation cost for its binding to macromolecular r...
Citation: Journal of Cheminformatics 2013 5:8 -
InChI - the worldwide chemical structure identifier standard
Since its public introduction in 2005 the IUPAC InChI chemical structure identifier standard has become the international, worldwide standard for defined chemical structures. This article will describe the ext...
Citation: Journal of Cheminformatics 2013 5:7 -
Chemical datuments as scientific enablers
This article is an attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal. An exploration of the interactions present in a small fragment of ...
Citation: Journal of Cheminformatics 2013 5:6 -
Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines
In order to better understand the structural features of natural compounds from traditional Chinese medicines, the scaffold architectures of drug-like compounds in MACCS-II Drug Data Report (MDDR), non-drug-li...
Citation: Journal of Cheminformatics 2013 5:5 -
Modeling of non-additive mixture properties using the Online CHEmical database and Modeling environment (OCHEM)
The Online Chemical Modeling Environment (OCHEM, http://ochem.eu) is a web-based platform that provides tools for automation of typical steps necessary to create a...
Citation: Journal of Cheminformatics 2013 5:4 -
UniChem: a unified chemical structure cross-referencing and identifier tracking system
UniChem is a freely available compound identifier mapping service on the internet, designed to optimize the efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based ...
Citation: Journal of Cheminformatics 2013 5:3 -
Enhanced ranking of PknB Inhibitors using data fusion methods
Mycobacterium tuberculosis encodes 11 putative serine-threonine proteins Kinases (STPK) which regulates transcription, cell development and interaction with the host cells. From the 11 STPKs three kinases name...
Citation: Journal of Cheminformatics 2013 5:2 -
PubChem3D: conformer ensemble accuracy
PubChem is a free and publicly available resource containing substance descriptions and their associated biological activity information. PubChem3D is an extension to PubChem containing computationally-derived...
Citation: Journal of Cheminformatics 2013 5:1 -
Automated compound classification using a chemical ontology
Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound ...
Citation: Journal of Cheminformatics 2012 4:40 -
InChIKey collision resistance: an experimental testing
InChIKey is a 27-character compacted (hashed) version of InChI which is intended for Internet and database searching/indexing and is based on an SHA-256 hash of the InChI character string. The first block of I...
Citation: Journal of Cheminformatics 2012 4:39 -
chemf: A purely functional chemistry toolkit
Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in ...
Citation: Journal of Cheminformatics 2012 4:38 -
Voting-based consensus clustering for combining multiple clusterings of chemical structures
Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few...
Citation: Journal of Cheminformatics 2012 4:37 -
Review of “Statistical Modelling of Molecular Descriptors in QSAR/QSPR” by Matthias Dehmer, Kurt Varmuza, and Danail Bonchev
Citation: Journal of Cheminformatics 2012 4:36 -
Consistency of systematic chemical identifiers within and between small-molecule databases
Correctness of structures and associated metadata within public and commercial chemical databases greatly impacts drug discovery research activities such as quantitative structure–property relationships modell...
Citation: Journal of Cheminformatics 2012 4:35 -
InChI: a user’s perspective
Exchange of chemical structures between practicing chemists is essential to chemical communication. The International Chemical Identifier (InChI) provides a means for lossless communication of structures witho...
Citation: Journal of Cheminformatics 2012 4:34 -
InChI: connecting and navigating chemistry
The International Chemical Identifier (InChI) has had a dramatic impact on providing a means by which to deduplicate, validate and link together chemical compounds and related information across databases. Its...
Citation: Journal of Cheminformatics 2012 4:33