Articles
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Citation: Journal of Cheminformatics 2014 6(Suppl 1):P41
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Identification of SUMO activating enzyme 1 inhibitors utilizing virtual screening approach
Citation: Journal of Cheminformatics 2014 6(Suppl 1):P37 -
Entropy gain due to water release upon ligand binding
Citation: Journal of Cheminformatics 2014 6(Suppl 1):P35 -
Scaffold hunter: visual analysis of biological activity data
Citation: Journal of Cheminformatics 2014 6(Suppl 1):P33 -
Making the most of approximate maximum common substructure search
Citation: Journal of Cheminformatics 2014 6(Suppl 1):P29 -
In silico polypharmacology: retrospective recognition vs. rational design
Citation: Journal of Cheminformatics 2014 6(Suppl 1):O25 -
Interaction studies of Alzheimer's Cathepsin B protein with inhibitors in presence and absence of water
Citation: Journal of Cheminformatics 2014 6(Suppl 1):P23 -
Analysis and visual summarization of molecular dynamics simulation
Citation: Journal of Cheminformatics 2014 6(Suppl 1):O16 -
Entropy in specificity and thermodynamics of binding
Citation: Journal of Cheminformatics 2014 6(Suppl 1):O8 -
Limits to molecular matched-pair analysis: the experimental uncertainty case
Citation: Journal of Cheminformatics 2014 6(Suppl 1):O6 -
Theoretical studies on cycloaddition reactions
Citation: Journal of Cheminformatics 2014 6(Suppl 1):P2 -
The use of 2D fingerprint methods to support the assessment of structural similarity in orphan drug legislation
In the European Union, medicines are authorised for some rare disease only if they are judged to be dissimilar to authorised orphan drugs for that disease. This paper describes the use of 2D fingerprints to sh...
Citation: Journal of Cheminformatics 2014 6:5 -
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing
Few environments have been developed or deployed to widely share biomolecular simulation data or to enable collaborative networks to facilitate data exploration and reuse. As the amount and complexity of data ...
Citation: Journal of Cheminformatics 2014 6:4 -
Efficient ring perception for the Chemistry Development Kit
The Chemistry Development Kit (CDK) is an open source Java library for manipulating and processing chemical information. A key aspect in handling chemical structures is the determination of the chemical rings....
Citation: Journal of Cheminformatics 2014 6:3 -
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2
An important step in the reconstruction of a metabolic network is annotation of metabolites. Metabolites are generally annotated with various database or structure based identifiers. Metabolite annotations in ...
Citation: Journal of Cheminformatics 2014 6:2 -
Prediction of novel drug indications using network driven biological data prioritization and integration
With the rapid development of high-throughput genomic technologies and the accumulation of genome-wide datasets for gene expression profiling and biological networks, the impact of diseases and drugs on gene e...
Citation: Journal of Cheminformatics 2014 6:1 -
First steps towards semantic descriptions of electronic laboratory notebook records
In order to exploit the vast body of currently inaccessible chemical information held in Electronic Laboratory Notebooks (ELNs) it is necessary not only to make it available but also to develop protocols for d...
Citation: Journal of Cheminformatics 2013 5:52 -
CVDHD: a cardiovascular disease herbal database for drug discovery and network pharmacology
Cardiovascular disease (CVD) is the leading cause of death and associates with multiple risk factors. Herb medicines have been used to treat CVD long ago in china and several natural products or derivatives (e...
Citation: Journal of Cheminformatics 2013 5:51 -
Improving structural similarity based virtual screening using background knowledge
Virtual screening in the form of similarity rankings is often applied in the early drug discovery process to rank and prioritize compounds from a database. This similarity ranking can be achieved with structur...
Citation: Journal of Cheminformatics 2013 5:50 -
Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases
‘Phylogenetic trees’ are commonly used for the analysis of chemogenomics datasets and to relate protein targets to each other, based on the (shared) bioactivities of their ligands. However, no real assessment ...
Citation: Journal of Cheminformatics 2013 5:49 -
Molecule database framework: a framework for creating database applications with chemical structure search capability
Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical struc...
Citation: Journal of Cheminformatics 2013 5:48 -
Complementary PLS and KNN algorithms for improved 3D-QSDAR consensus modeling of AhR binding
Multiple validation techniques (Y-scrambling, complete training/test set randomization, determination of the dependence of R2test on the number of randomization cycles, etc.) aimed to improve the reliability of t...
Citation: Journal of Cheminformatics 2013 5:47 -
CH5M3D: an HTML5 program for creating 3D molecular structures
While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason...
Citation: Journal of Cheminformatics 2013 5:46 -
International chemical identifier for reactions (RInChI)
The IUPAC International Chemical Identifier (InChI) provides a method to generate a unique text descriptor of molecular structures. Building on this work, we report a process to generate a unique text descript...
Citation: Journal of Cheminformatics 2013 5:45 -
Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribu...
Citation: Journal of Cheminformatics 2013 5:44 -
Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods
Fingerprint similarity is a common method for comparing chemical structures. Similarity is an appealing approach because, with many fingerprint types, it provides intuitive results: a chemist looking at two mo...
Citation: Journal of Cheminformatics 2013 5:43 -
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets
While a large body of work exists on comparing and benchmarking descriptors of molecular structures, a similar comparison of protein descriptor sets is lacking. Hence, in the current work a total of 13 amino a...
Citation: Journal of Cheminformatics 2013 5:42 -
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets
While a large body of work exists on comparing and benchmarking of descriptors of molecular structures, a similar comparison of protein descriptor sets is lacking. Hence, in the current work a total of 13 diff...
Citation: Journal of Cheminformatics 2013 5:41 -
LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions
2D diagrams are widely used in the scientific literature to represent interactions between ligands and biomacromolecules. Such schematic diagrams are very helpful to better understand the chemical interactions...
Citation: Journal of Cheminformatics 2013 5:40 -
MONA – Interactive manipulation of molecule collections
Working with small‐molecule datasets is a routine task forcheminformaticians and chemists. The analysis and comparison of vendorcatalogues and the compilation of promising candidates as starting pointsfor scre...
Citation: Journal of Cheminformatics 2013 5:38 -
Full “Laplacianised” posterior naive Bayesian algorithm
In the last decade the standard Naive Bayes (SNB) algorithm has been widely employed in multi–class classification problems in cheminformatics. This popularity is mainly due to the fact that the algorithm is s...
Citation: Journal of Cheminformatics 2013 5:37 -
MOLE 2.0: advanced approach for analysis of biomacromolecular channels
Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity.
Citation: Journal of Cheminformatics 2013 5:39 -
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites
Many Protein Data Bank (PDB) users assume that the deposited structural models are of high quality but forget that these models are derived from the interpretation of experimental data. The accuracy of atom co...
Citation: Journal of Cheminformatics 2013 5:36 -
Rubabel: wrapping open Babel with Ruby
The number and diversity of wrappers for chemoinformatic toolkits suggests the diverse needs of the chemoinformatic community. While existing chemoinformatics libraries provide a broad range of utilities, many...
Citation: Journal of Cheminformatics 2013 5:35 -
A big data approach to the ultra-fast prediction of DFT-calculated bond energies
The rapid access to intrinsic physicochemical properties of molecules is highly desired for large scale chemical data mining explorations such as mass spectrum prediction in metabolomics, toxicity risk assessm...
Citation: Journal of Cheminformatics 2013 5:34 -
Inferring multi-target QSAR models with taxonomy-based multi-task learning
A plethora of studies indicate that the development of multi-target drugs is beneficial for complex diseases like cancer. Accurate QSAR models for each of the desired targets assist the optimization of a lead ...
Citation: Journal of Cheminformatics 2013 5:33 -
Cheminformatics for the masses: a chance to increase educational opportunities for the next generation of cheminformaticians
Citation: Journal of Cheminformatics 2013 5:32 -
Predicting the protein targets for athletic performance-enhancing substances
The World Anti-Doping Agency (WADA) publishes the Prohibited List, a manually compiled international standard of substances and methods prohibited in-competition, out-of-competition and in particular sports. I...
Citation: Journal of Cheminformatics 2013 5:31 -
Drug repositioning: a machine-learning approach through data integration
Existing computational methods for drug repositioning either rely only on the gene expression response of cell lines after treatment, or on drug-to-disease relationships, merging several information levels. Ho...
Citation: Journal of Cheminformatics 2013 5:30 -
Review of “Contemporary computer-assisted approaches to molecular structure elucidation (new developments in NMR)” by Mikhail E Elyashberg, Antony Williams and Kirill Blinov
Citation: Journal of Cheminformatics 2013 5:29 -
HIM-herbal ingredients in-vivo metabolism database
Herbal medicine has long been viewed as a valuable asset for potential new drug discovery and herbal ingredients’ metabolites, especially the in vivo metabolites were often found to gain better pharmacological, p...
Citation: Journal of Cheminformatics 2013 5:28 -
Defining a novel k-nearest neighbours approach to assess the applicability domain of a QSAR model for reliable predictions
With the growing popularity of using QSAR predictions towards regulatory purposes, such predictive models are now required to be strictly validated, an essential feature of which is to have the model’s Applica...
Citation: Journal of Cheminformatics 2013 5:27 -
Open-source platform to benchmark fingerprints for ligand-based virtual screening
Similarity-search methods using molecular fingerprints are an important tool for ligand-based virtual screening. A huge variety of fingerprints exist and their performance, usually assessed in retrospective be...
Citation: Journal of Cheminformatics 2013 5:26 -
From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language
Multidisciplinary integrated research requires the ability to couple thediverse sets of data obtained from a range of complex experiments andcomputer simulations. Integrating data requires semantically richinf...
Citation: Journal of Cheminformatics 2013 5:25 -
JSME: a free molecule editor in JavaScript
A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser ...
Citation: Journal of Cheminformatics 2013 5:24 -
The ChEMBL database as linked open data
Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Un...
Citation: Journal of Cheminformatics 2013 5:23 -
In-silico design of computational nucleic acids for molecular information processing
Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the ...
Citation: Journal of Cheminformatics 2013 5:22 -
A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding
A tandem technique of hard equipment is often used for the chemical analysis of a single cell to first isolate and then detect the wanted identities. The first part is the separation of wanted chemicals from t...
Citation: Journal of Cheminformatics 2013 5:21 -
Extracting and connecting chemical structures from text sources using chemicalize.org
Exploring bioactive chemistry requires navigating between structures and data from a variety of text-based sources. While PubChem currently includes approximately 16 million document-extracted structures (15 m...
Citation: Journal of Cheminformatics 2013 5:20 -
Druggable chemical space and enumerative combinatorics
There is a growing body of literature describing the properties of marketed drugs, the concept of drug-likeness and the vastness of chemical space. In that context, enumerative combinatorics with simple atomic...
Citation: Journal of Cheminformatics 2013 5:19