Articles
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Citation: Journal of Cheminformatics 2010 2(Suppl 1):P53
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Get the best from substructure mining
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P51 -
Ionotropic GABA receptors: modelling and design of selective ligands
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P49 -
Adaptive matrix metrics for molecular descriptor assessment in QSPR classification
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P47 -
QSAR of anti-inflammatory drugs
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P45 -
A combined combinatorial and pKa-based approach to ligand protonation states
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P43 -
Applicability domain for classification problems
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P41 -
Expanding and understanding metabolite space
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P39 -
A comparative study of in silico prediction of pKa
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P37 -
Prediction of highly-connected 'hub'-proteins in protein interaction networks using QSAR
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P35 -
Systematic extraction of structure-activity relationship information from biological screening data
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P22 -
DrugScorePPI for scoring protein-protein interactions: improving a knowledge-based scoring function by atomtype-based QSAR
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P20 -
Bioisosteric similarity of drugs in virtual screening
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P18 -
Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P16 -
Molecular fragments chemoinformatics
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P14 -
Random molecular substructures as fragment-type descriptors
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O12 -
Protein negative/positively cooperative binding to zwitterionic/anionic vesicles
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P12 -
3D pharmacophore alignments: does improved geometric accuracy affect virtual screening performance?
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O10 -
Modelling dissociation constants of organic acids by local molecular parameters
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P10 -
Embedded infrastructure for primary data in chemistry
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P8 -
ChEBI: a chemistry ontology and database
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P6 -
Mining public-source databases for structure-activity relationships
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P4 -
Molecular bioactivity extrapolation to novel targets by support vector machines
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O3 -
OrChem
Citation: Journal of Cheminformatics 2010 2(Suppl 1):F3 -
Systems chemistry: from chemical self-replication to trisoligo-based nanoconstruction
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O1 -
Bingo from SciTouch LLC: chemistry cartridge for Oracle database
Citation: Journal of Cheminformatics 2010 2(Suppl 1):F1 -
Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining
Previously, we developed a combined dictionary dubbed Chemlist for the identification of small molecules and drugs in text based on a number of publicly available databases and tested it on an annotated corpus...
Citation: Journal of Cheminformatics 2010 2:3 -
Estimation of the applicability domain of kernel-based machine learning models for virtual screening
The virtual screening of large compound databases is an important application of structural-activity relationship models. Due to the high structural diversity of these data sets, it is impossible for machine l...
Citation: Journal of Cheminformatics 2010 2:2 -
Molecular structure input on the web
A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editor...
Citation: Journal of Cheminformatics 2010 2:1 -
Interpretable correlation descriptors for quantitative structure-activity relationships
The topological maximum cross correlation (TMACC) descriptors are alignment-independent 2D descriptors for the derivation of QSARs. TMACC descriptors are generated using atomic properties determined by molecul...
Citation: Journal of Cheminformatics 2009 1:22 -
Virtual screening of bioassay data
There are three main problems associated with the virtual screening of bioassay data. The first is access to freely-available curated data, the second is the number of false positives that occur in the physica...
Citation: Journal of Cheminformatics 2009 1:21 -
The PubChem chemical structure sketcher
PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandator...
Citation: Journal of Cheminformatics 2009 1:20 -
Application of 3D Zernike descriptors to shape-based ligand similarity searching
The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognit...
Citation: Journal of Cheminformatics 2009 1:19 -
Software platform virtualization in chemistry research and university teaching
Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it ...
Citation: Journal of Cheminformatics 2009 1:18 -
OrChem - An open source chemistry search engine for Oracle®
Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engine...
Citation: Journal of Cheminformatics 2009 1:17 -
Shape: automatic conformation prediction of carbohydrates using a genetic algorithm
Detailed experimental three dimensional structures of carbohydrates are often difficult to acquire. Molecular modelling and computational conformation prediction are therefore commonly used tools for three dim...
Citation: Journal of Cheminformatics 2009 1:16 -
Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock
Molecular docking methods are commonly used for predicting binding modes and energies of ligands to proteins. For accurate complex geometry and binding energy estimation, an appropriate method for calculating ...
Citation: Journal of Cheminformatics 2009 1:15 -
Optimal assignment methods for ligand-based virtual screening
Ligand-based virtual screening experiments are an important task in the early drug discovery stage. An ambitious aim in each experiment is to disclose active structures based on new scaffolds. To perform these...
Citation: Journal of Cheminformatics 2009 1:14 -
Fast automated placement of polar hydrogen atoms in protein-ligand complexes
Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the pos...
Citation: Journal of Cheminformatics 2009 1:13 -
Small Molecule Subgraph Detector (SMSD) toolkit
Finding one small molecule (query) in a large target library is a challenging task in computational chemistry. Although several heuristic approaches are available using fragment-based chemical similarity searc...
Citation: Journal of Cheminformatics 2009 1:12 -
DPRESS: Localizing estimates of predictive uncertainty
The need to have a quantitative estimate of the uncertainty of prediction for QSAR models is steadily increasing, in part because such predictions are being widely distributed as tabulated values disconnected ...
Citation: Journal of Cheminformatics 2009 1:11 -
Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds
Since 2004 public cheminformatic databases and their collective functionality for exploring relationships between compounds, protein sequences, literature and assay data have advanced dramatically. In parallel...
Citation: Journal of Cheminformatics 2009 1:10 -
The Spectral Game: leveraging Open Data and crowdsourcing for education
We report on the implementation of the Spectral Game, a web-based game where players try to match molecules to various forms of interactive spectra including 1D/2D NMR, Mass Spectrometry and Infrared spectra. ...
Citation: Journal of Cheminformatics 2009 1:9 -
Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions
A method to estimate ease of synthesis (synthetic accessibility) of drug-like molecules is needed in many areas of the drug discovery process. The development and validation of such a method that is able to ch...
Citation: Journal of Cheminformatics 2009 1:8 -
Large scale study of multiple-molecule queries
In ligand-based screening, as well as in other chemoinformatics applications, one seeks to effectively search large repositories of molecules in order to retrieve molecules that are similar typically to a sing...
Citation: Journal of Cheminformatics 2009 1:7 -
Combining docking with pharmacophore filtering for improved virtual screening
Virtual screening is used to distinguish potential leads from inactive compounds in a database of chemical samples. One method for accomplishing this is by docking compounds into the structure of a receptor bi...
Citation: Journal of Cheminformatics 2009 1:6 -
Evaluation of a Bayesian inference network for ligand-based virtual screening
Bayesian inference networks enable the computation of the probability that an event will occur. They have been used previously to rank textual documents in order of decreasing relevance to a user-defined query...
Citation: Journal of Cheminformatics 2009 1:5 -
A constructive approach for discovering new drug leads: Using a kernel methodology for the inverse-QSAR problem
The inverse-QSAR problem seeks to find a new molecular descriptor from which one can recover the structure of a molecule that possess a desired activity or property. Surprisingly, there are very few papers pro...
Citation: Journal of Cheminformatics 2009 1:4 -
Chemistry publication – making the revolution
The advent of the Internet has been the impetus for the Open Access movement, a movement focused on expanding access to information principally by reducing the costs of journals. I argue here that the Open Acc...
Citation: Journal of Cheminformatics 2009 1:2 -
Grand challenges for cheminformatics
Citation: Journal of Cheminformatics 2009 1:1