Articles
Page 20 of 29
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Citation: Journal of Cheminformatics 2013 5:29
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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 -
Predicting pK a values from EEM atomic charges
The acid dissociation constant p K a is a very important molecular property, and there is a strong interest in the development of reliable and fast methods for p K ...
Citation: Journal of Cheminformatics 2013 5:18 -
The influence of the inactives subset generation on the performance of machine learning methods
A growing popularity of machine learning methods application in virtual screening, in both classification and regression tasks, can be observed in the past few years. However, their effectiveness is strongly d...
Citation: Journal of Cheminformatics 2013 5:17 -
Pt(II) and Pt(IV) complexes with large hydrophobic ligands: a study of new potential cytostatics
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P52 -
Rationalisation and visualisation of non-bonded interactions
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P48 -
Predicting the protein localization sites using artificial neural networks
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P46 -
Enalos KNIME nodes: exploring environmental durability, ageing resistance and corrosion inhibition
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P42 -
A 3D-QSAR model for cannabinoid receptor (CB2) ligands derived from aligned pharmacophors
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P40 -
PubChem: atom environments for molecule standardization
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P38 -
The FPS fingerprint format and chemfp toolkit
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P36 -
Using machine learning techniques for rationalising phenotypic readouts from a rat sleeping model
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P34 -
Pairwise structural comparison of tiagabine analogs gives new insights into their protein binding modes
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P32 -
The influence of training actives/inactives ratio on machine learning performance
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P30 -
Application of Structural Interaction Fingerpints (SIFts) into post-docking analysis - insight into activity and selectivity
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P28 -
Combining SFCscore with Random Forests leads to improved affinity prediction for protein-ligand complexes
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P27 -
Relating GPCRs pharmacological space based on ligands chemical similarities
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P26 -
The influence of hashed fingerprints density on the machine learning methods performance
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P25 -
Chemogenomic approach to increase accuracy of QSAR modeling of inhibition activity against five major P450 isoforms
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P23 -
MycPermCheck: the Mycobacterium tuberculosispermeability prediction tool for small molecules
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P21 -
A next-generation chemistry database cartridge
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P19 -
Development of a pharmacorphore model for pharmacological chaperones targeting mutant trafficking-deficient CNG channels
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O18 -
Challenges in agrochemicals design
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O17 -
Combination of fingerprints and MCS-based (inSARa) networks for Structure-Activity-Relationship analysis
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P17 -
Efficient maximum common subgraph (MCS) searching of large chemical databases
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O15 -
Annotating targets with pathways: extending approaches to mode of action analysis
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P15 -
3D-QSAR reloaded: Open3DALIGN meets COSMOsar3D
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O13 -
Simulation of transport processes and chemical reactions in building materials
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P13 -
Theoretical and experimental study of the pH-dependent interaction of amino acids and MFI-type zeolite
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O11 -
ParaDockS - an open-source framework for molecular docking: implementation of target-class-specific scoring methods
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P11 -
The importance of template choice in homology modeling. A 5-HT6R case study
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P8 -
Let's talk about rings
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O8 -
PREDator - a new structure-based approach for cross-reactivity predictions
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P6 -
FMCS: a novel algorithm for the multiple MCS problem
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O6 -
Molecular simulations of peptides and proteins with Molecular Fragment Dynamics (MFD)
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P4 -
Reproducibility in cheminformatics and computational chemistry research: certainly we can do better than this
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O4 -
The MoSGrid - e-science gateway: molecular simulations in a distributed computing environment
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O3 -
In silico characterization of the motor subunit of the e.coli. restriction-modification system EcoR1241
Citation: Journal of Cheminformatics 2013 5(Suppl 1):P2 -
Protein modeling and molecular dynamic studies of two new surfactant proteins
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O2 -
Targeting protein dynamics in drug design
Citation: Journal of Cheminformatics 2013 5(Suppl 1):O1 -
Get your chemistry right with KNIME
Citation: Journal of Cheminformatics 2013 5(Suppl 1):F1