Articles
Page 25 of 30
-
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P50
-
Docking based 3D-QSAR studies applied at the BRAF inhibitors to understand the binding mechanism
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P46 -
INSARA: a new method for the analysis and visualization of Structure-Activity-Relationships
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P44 -
Postprocessing of molecular docking poses using binding free energy calculations
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P42 -
Probabilistic classifier: generated using randomised sub-sampling of the feature space
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P40 -
Adsorption of amino acids on MFI-type zeolite: DFT calculations and experimental results
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P38 -
Systematic search for pairwise dependencies of torsion angles
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P36 -
Synergistic approach of structure-based and ligand-based drug design for the development of selective cannabinod receptor ligands
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P11 -
Mechanistic DFT studies – helicate-type complexes with different alcylic spacers
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P9 -
Assessment of a probabilistic framework for combining structure- and ligand-based virtual screening
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P7 -
Structured chemical class definitions and automated matching for chemical ontology evolution
Citation: Journal of Cheminformatics 2012 4(Suppl 1):P5 -
Packaging free software chemistry programs in Debian GNU/Linux: past, present and future
Citation: Journal of Cheminformatics 2012 4(Suppl 1):F4 -
What's new in KNIME?
Citation: Journal of Cheminformatics 2012 4(Suppl 1):F2 -
GCC2011 – 25 years of computational chemistry meetings
Citation: Journal of Cheminformatics 2012 4(Suppl 1):A1 -
Structure-based classification and ontology in chemistry
Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those ...
Citation: Journal of Cheminformatics 2012 4:8 -
CheS-Mapper - Chemical Space Mapping and Visualization in 3D
Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical co...
Citation: Journal of Cheminformatics 2012 4:7 -
Improving integrative searching of systems chemical biology data using semantic annotation
Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry an...
Citation: Journal of Cheminformatics 2012 4:6 -
Blind trials of computer-assisted structure elucidation software
One of the largest challenges in chemistry today remains that of efficiently mining through vast amounts of data in order to elucidate the chemical structure for an unknown compound. The elucidated candidate c...
Citation: Journal of Cheminformatics 2012 4:5 -
A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space
The current chemical space of known small molecules is estimated to exceed 1060 structures. Though the largest physical compound repositories contain only a few tens of millions of unique compounds, virtual scree...
Citation: Journal of Cheminformatics 2012 4:4 -
LICSS - a chemical spreadsheet in microsoft excel
Representations of chemical datasets in spreadsheet format are important for ready data assimilation and manipulation. In addition to the normal spreadsheet facilities, chemical spreadsheets need to have visua...
Citation: Journal of Cheminformatics 2012 4:3 -
Predicting the mechanism of phospholipidosis
The mechanism of phospholipidosis is still not well understood. Numerous different mechanisms have been proposed, varying from direct inhibition of the breakdown of phospholipids to the binding of a drug compo...
Citation: Journal of Cheminformatics 2012 4:2 -
Making SharePoint® Chemically Aware™
The use of SharePoint® collaboration software for content management has become a critical part of today's drug discovery process. SharePoint 2010 software has laid a foundation which enables researchers to colla...
Citation: Journal of Cheminformatics 2012 4:1 -
New developments on the cheminformatics open workflow environment CDK-Taverna
The computational processing and analysis of small molecules is at heart of cheminformatics and structural bioinformatics and their application in e.g. metabolomics or drug discovery. Pipelining or workflow to...
Citation: Journal of Cheminformatics 2011 3:54 -
MyChemise: A 2D drawing program that uses morphing for visualisation purposes
MyChemise (My Chemical Structure Editor) is a new 2D structure editor. It is designed as a Java applet that enables the direct creation of structures in the Internet using a web browser. MyChemise saves files ...
Citation: Journal of Cheminformatics 2011 3:53 -
Automated annotation of chemical names in the literature with tunable accuracy
A significant portion of the biomedical and chemical literature refers to small molecules. The accurate identification and annotation of compound name that are relevant to the topic of the given literature can...
Citation: Journal of Cheminformatics 2011 3:52 -
An investigation into pharmaceutically relevant mutagenicity data and the influence on Ames predictive potential
In drug discovery, a positive Ames test for bacterial mutation presents a significant hurdle to advancing a drug to clinical trials. In a previous paper, we discussed success in predicting the genotoxicity of ...
Citation: Journal of Cheminformatics 2011 3:51 -
2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope
Quantitative structure-activity relationships (QSAR) analysis of peptides is helpful for designing various types of drugs such as kinase inhibitor or antigen. Capturing various properties of peptides is essent...
Citation: Journal of Cheminformatics 2011 3:50 -
Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain
The Elk-1 transcription factor is a member of a group of proteins called ternary complex factors, which serve as a paradigm for gene regulation in response to extracellular signals. Its deregulation has been l...
Citation: Journal of Cheminformatics 2011 3:49 -
Semantic science and its communication - a personal view
The articles in this special issue represent the culmination of about 15 years working with the potential of the web to support chemical and related subjects. The selection of papers arises from a symposium he...
Citation: Journal of Cheminformatics 2011 3:48 -
Open Bibliography for Science, Technology, and Medicine
The concept of Open Bibliography in science, technology and medicine (STM) is introduced as a combination of Open Source tools, Open specifications and Open bibliographic data. An Openly searchable and navigab...
Citation: Journal of Cheminformatics 2011 3:47 -
The past, present and future of Scientific discourse
The science journal is 346 years old in 2011, having evolved continuously but largely incrementally over that period. Its reinvention for an online presence has largely preserved its previously printed nature,...
Citation: Journal of Cheminformatics 2011 3:46 -
Ami - The chemist's amanuensis
The Ami project was a six month Rapid Innovation project sponsored by JISC to explore the Virtual Research Environment space. The project brainstormed with chemists and decided to investigate ways to facilitat...
Citation: Journal of Cheminformatics 2011 3:45 -
CML: Evolution and design
A retrospective view of the design and evolution of Chemical Markup Language (CML) is presented by its original authors.
Citation: Journal of Cheminformatics 2011 3:44 -
The semantics of Chemical Markup Language (CML): dictionaries and conventions
The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-proc...
Citation: Journal of Cheminformatics 2011 3:43 -
The semantic architecture of the World-Wide Molecular Matrix (WWMM)
The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been ins...
Citation: Journal of Cheminformatics 2011 3:42 -
OSCAR4: a flexible architecture for chemical text-mining
The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work has resulted in the ...
Citation: Journal of Cheminformatics 2011 3:41 -
Mining chemical information from open patents
Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is ...
Citation: Journal of Cheminformatics 2011 3:40 -
CMLLite: a design philosophy for CML
CMLLite is a collection of definitions and processes which provide strong and flexible validation for a document in Chemical Markup Language (CML). It consists of an updated CML schema (schema3), conventions s...
Citation: Journal of Cheminformatics 2011 3:39 -
The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age
Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of...
Citation: Journal of Cheminformatics 2011 3:38 -
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by prom...
Citation: Journal of Cheminformatics 2011 3:37 -
Openness as infrastructure
The advent of open access to peer reviewed scholarly literature in the biomedical sciences creates the opening to examine scholarship in general, and chemistry in particular, to see where and how novel forms o...
Citation: Journal of Cheminformatics 2011 3:36 -
Three stories about the conduct of science: Past, future, and present
In this piece I would like to tell a few stories; three stories to be precise. Firstly I want to explain where I am, where I've come from and what has led me to the views that I hold today. I find myself at an...
Citation: Journal of Cheminformatics 2011 3:35 -
Adventures in public data
This article contains the slides and transcript of a talk given by Dan Zaharevitz at the "Visions of a Semantic Molecular Future" symposium held at the University of Cambridge Department of Chemistry on 2011-0...
Citation: Journal of Cheminformatics 2011 3:34 -
Open Babel: An open chemical toolbox
A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto ...
Citation: Journal of Cheminformatics 2011 3:33 -
PubChem3D: a new resource for scientists
PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an eff...
Citation: Journal of Cheminformatics 2011 3:32 -
Statistical filtering for NMR based structure generation
The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The difficulty of a structure elucidation problem depends more on the typ...
Citation: Journal of Cheminformatics 2011 3:31 -
Structural diversity of biologically interesting datasets: a scaffold analysis approach
The recent public availability of the human metabolome and natural product datasets has revitalized "metabolite-likeness" and "natural product-likeness" as a drug design concept to design lead libraries target...
Citation: Journal of Cheminformatics 2011 3:30 -
Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision
Data fusion methods are widely used in virtual screening, and make the implicit assumption that the more often a molecule is retrieved in multiple similarity searches, the more likely it is to be active. This ...
Citation: Journal of Cheminformatics 2011 3:29 -
AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment
Machine learning has a vast range of applications. In particular, advanced machine learning methods are routinely and increasingly used in quantitative structure activity relationship (QSAR) modeling. QSAR dat...
Citation: Journal of Cheminformatics 2011 3:28 -
Theoretical NMR correlations based Structure Discussion
The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more o...
Citation: Journal of Cheminformatics 2011 3:27