Articles
Page 27 of 29
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Citation: Journal of Cheminformatics 2011 3(Suppl 1):P33
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HYDEing the false positives – scoring for lead optimization
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P29 -
Virtual screening using structure-based consensus pharmacophore models and ensemble docking based on MD-generated conformations
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O23 -
WizePairZ: a novel algorithm to identify, encode, and exploit matched molecular pairs with unspecified cores in medicinal chemistry
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O9 -
Representation of Markush structures: from molecules toward patents
Citation: Journal of Cheminformatics 2011 3(Suppl 1):O7 -
Ketcher: web-based chemical structure editor
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P3 -
German Conference on Chemoinformatics 2010 – organizers' notes
Citation: Journal of Cheminformatics 2011 3(Suppl 1):I1 -
Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods
Citation: Journal of Cheminformatics 2011 3(Suppl 1):P1 -
Interpreting linear support vector machine models with heat map molecule coloring
Model-based virtual screening plays an important role in the early drug discovery stage. The outcomes of high-throughput screenings are a valuable source for machine learning algorithms to infer such models. B...
Citation: Journal of Cheminformatics 2011 3:11 -
Review of "Data Analysis with Open Source Tools" by Philipp K Janert
Citation: Journal of Cheminformatics 2011 3:10 -
PubChem3D: Diversity of shape
The shape diversity of 16.4 million biologically relevant molecules from the PubChem Compound database and their 1.46 billion diverse conformers was explored as a function of molecular volume.
Citation: Journal of Cheminformatics 2011 3:9 -
Confab - Systematic generation of diverse low-energy conformers
Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-ene...
Citation: Journal of Cheminformatics 2011 3:8 -
Use of structure-activity landscape index curves and curve integrals to evaluate the performance of multiple machine learning prediction models
Standard approaches to address the performance of predictive models that used common statistical measurements for the entire data set provide an overview of the average performance of the models across the ent...
Citation: Journal of Cheminformatics 2011 3:7 -
FlaME: Flash Molecular Editor - a 2D structure input tool for the web
So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure edit...
Citation: Journal of Cheminformatics 2011 3:6 -
Modular Chemical Descriptor Language (MCDL): Stereochemical modules
In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure...
Citation: Journal of Cheminformatics 2011 3:5 -
PubChem3D: Conformer generation
PubChem, an open archive for the biological activities of small molecules, provides search and analysis tools to assist users in locating desired information. Many of these tools focus on the notion of chemica...
Citation: Journal of Cheminformatics 2011 3:4 -
jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints
The decomposition of a chemical graph is a convenient approach to encode information of the corresponding organic compound. While several commercial toolkits exist to encode molecules as so-called fingerprints...
Citation: Journal of Cheminformatics 2011 3:3 -
Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method
The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex m...
Citation: Journal of Cheminformatics 2011 3:2 -
CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures
CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and ...
Citation: Journal of Cheminformatics 2011 3:1 -
Predicting cytotoxicity from heterogeneous data sources with Bayesian learning
We collected data from over 80 different cytotoxicity assays from Pfizer in-house work as well as from public sources and investigated the feasibility of using these datasets, which come from a variety of assa...
Citation: Journal of Cheminformatics 2010 2:11 -
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters
Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clu...
Citation: Journal of Cheminformatics 2010 2:10 -
Organization of GC/MS and LC/MS metabolomics data into chemical libraries
Metabolomics experiments involve generating and comparing small molecule (metabolite) profiles from complex mixture samples to identify those metabolites that are modulated in altered states (e.g., disease, dr...
Citation: Journal of Cheminformatics 2010 2:9 -
Basic primitives for molecular diagram sketching
A collection of primitive operations for molecular diagram sketching has been developed. These primitives compose a concise set of operations which can be used to construct publication-quality 2 D coordinates ...
Citation: Journal of Cheminformatics 2010 2:8 -
Collaborative development of predictive toxicology applications
OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical...
Citation: Journal of Cheminformatics 2010 2:7 -
WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications
In recent years, there has been a huge increase in the amount of publicly-available and proprietary information pertinent to drug discovery. However, there is a distinct lack of data mining tools available to ...
Citation: Journal of Cheminformatics 2010 2:6 -
Towards interoperable and reproducible QSAR analyses: Exchange of datasets
QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, bu...
Citation: Journal of Cheminformatics 2010 2:5 -
Erratum to: Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining
Citation: Journal of Cheminformatics 2010 2:4 -
Classification of CYP450 1A2 inhibitors using PubChem data
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P40 -
Efficient extraction of canonical spatial relationships using a recursive enumeration of k-subsets
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P36 -
Progress on an open source computer-assisted structure elucidation suite (SENECA)
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P34 -
Ligand-side tautomer enumeration and scoring for structure-based drug-design
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P32 -
Learning antibacterial activity against S. Aureus on the Chimiothèque Nationale dataset
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P30 -
OrChem: an open source chemistry search engine for Oracle
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P28 -
Picking out polymorphs: H-bond prediction and crystal structure stability
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P26 -
Fleksy: a flexible approach to induced fit docking
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O24 -
Virtual screening by high-throughput docking using hydrogen bonding constraints for targeting a protein-protein interface in M. tuberculosis
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P24 -
Approaching the limits: scoring functions for affinity prediction
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O22 -
The membrane bound aromatic p-hydroxybenzoic acid oligoprenyltransferase (UbiA) - how iterative improvements lead to a realistic structure that offers new insights into functional aspects of prenyl transferases and terpene synthases
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O20 -
Personalized information spaces: improved access to chemical digital libraries
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O18 -
ChemSpider - building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O16 -
Biomaterialcoatings - a challenging task studied by the molecular fragment dynamics
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O14 -
KnowledgeSpace - a publicly available virtual chemistry space
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O9 -
Comparing manual and automated extraction of chemical entities from documents
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P7 -
Quantifying model errors using similarity to training data
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O7 -
OCHEM - on-line CHEmical database & modeling environment
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P5 -
Cross-validation is dead. Long live cross-validation! Model validation based on resampling
Citation: Journal of Cheminformatics 2010 2(Suppl 1):O5 -
jsMolEditor: an open source molecule editor for the next generation web
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P3 -
Dingo: 2D molecule and reaction structural formula rendering library
Citation: Journal of Cheminformatics 2010 2(Suppl 1):F2 -
CWM global search - an internet search engine for the chemist
Citation: Journal of Cheminformatics 2010 2(Suppl 1):P1 -
5th German Conference on Chemoinformatics: 23. CIC-Workshop. November 8-10, 2009, Goslar, Germany
Citation: Journal of Cheminformatics 2010 2(Suppl 1):A1