Volume 3, issue 1, December 2011
54 articles in this issue
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MyChemise: A 2D drawing program that uses morphing for visualisation purposes
Authors
- Jörg-Hubertus Wilhelm
- Content type: Software
- Open Access
- Published: 12 December 2011
- Article: 53
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Automated annotation of chemical names in the literature with tunable accuracy
Authors (first, second and last of 4)
- Jun D Zhang
- Lewis Y Geer
- Stephen H Bryant
- Content type: Research article
- Open Access
- Published: 22 November 2011
- Article: 52
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An investigation into pharmaceutically relevant mutagenicity data and the influence on Ames predictive potential
Authors
- Patrick McCarren
- Clayton Springer
- Lewis Whitehead
- Content type: Research article
- Open Access
- Published: 22 November 2011
- Article: 51
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2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope
Authors
- Tsutomu Osoda
- Satoru Miyano
- Content type: Research article
- Open Access
- Published: 02 November 2011
- Article: 50
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Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain
Authors
- Abrar Hussain
- Peter E Shaw
- Jonathan D Hirst
- Content type: Research article
- Open Access
- Published: 01 November 2011
- Article: 49
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Semantic science and its communication - a personal view
Authors
- Peter Murray-Rust
- Content type: Editorial
- Open Access
- Published: 14 October 2011
- Article: 48
This is part of 1 collection: -
Open Bibliography for Science, Technology, and Medicine
Authors (first, second and last of 7)
- Richard Jones
- Mark MacGillivray
- William Waites
- Content type: Research article
- Open Access
- Published: 14 October 2011
- Article: 47
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The past, present and future of Scientific discourse
Authors
- Henry S Rzepa
- Content type: Research article
- Open Access
- Published: 14 October 2011
- Article: 46
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Ami - The chemist's amanuensis
Authors (first, second and last of 9)
- Brian J Brooks
- Adam L Thorn
- Peter Murray-Rust
- Content type: Research article
- Open Access
- Published: 14 October 2011
- Article: 45
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CML: Evolution and design
Authors
- Peter Murray-Rust
- Henry S Rzepa
- Content type: Research article
- Open Access
- Published: 14 October 2011
- Article: 44
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The semantics of Chemical Markup Language (CML): dictionaries and conventions
Authors (first, second and last of 5)
- Peter Murray-Rust
- Joe A Townsend
- Jens Thomas
- Content type: Research article
- Open Access
- Published: 14 October 2011
- Article: 43
This is part of 1 collection: -
The semantic architecture of the World-Wide Molecular Matrix (WWMM)
Authors (first, second and last of 5)
- Peter Murray-Rust
- Sam E Adams
- Yong Zhang
- Content type: Research article
- Open Access
- Published: 14 October 2011
- Article: 42
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OSCAR4: a flexible architecture for chemical text-mining
Authors (first, second and last of 5)
- David M Jessop
- Sam E Adams
- Peter Murray-Rust
- Content type: Software
- Open Access
- Published: 14 October 2011
- Article: 41
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Mining chemical information from open patents
Authors
- David M Jessop
- Sam E Adams
- Peter Murray-Rust
- Content type: Research article
- Open Access
- Published: 14 October 2011
- Article: 40
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CMLLite: a design philosophy for CML
Authors
- Joe A Townsend
- Peter Murray-Rust
- Content type: Research article
- Open Access
- Published: 14 October 2011
- Article: 39
This is part of 1 collection: -
The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age
Authors (first, second and last of 9)
- Sam Adams
- Pablo de Castro
- Joe Townsend
- Content type: Research article
- Open Access
- Published: 14 October 2011
- Article: 38
This is part of 1 collection: -
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
Authors (first, second and last of 23)
- Noel M O'Boyle
- Rajarshi Guha
- Peter Murray-Rust
- Content type: Research article
- Open Access
- Published: 14 October 2011
- Article: 37
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Openness as infrastructure
Authors
- John Wilbanks
- Content type: Commentary
- Open Access
- Published: 14 October 2011
- Article: 36
This is part of 1 collection: -
Three stories about the conduct of science: Past, future, and present
Authors
- Cameron Neylon
- Content type: Commentary
- Open Access
- Published: 14 October 2011
- Article: 35
This is part of 1 collection: -
Adventures in public data
Authors
- Dan W Zaharevitz
- Content type: Oral presentation
- Open Access
- Published: 14 October 2011
- Article: 34
This is part of 1 collection: -
Open Babel: An open chemical toolbox
Authors (first, second and last of 6)
- Noel M O'Boyle
- Michael Banck
- Geoffrey R Hutchison
- Content type: Software
- Open Access
- Published: 07 October 2011
- Article: 33
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PubChem3D: a new resource for scientists
Authors (first, second and last of 13)
- Evan E Bolton
- Jie Chen
- Stephen H Bryant
- Content type: Software
- Open Access
- Published: 20 September 2011
- Article: 32
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Statistical filtering for NMR based structure generation
Authors
- Jochen Junker
- Content type: Preliminary communication
- Open Access
- Published: 11 August 2011
- Article: 31
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Structural diversity of biologically interesting datasets: a scaffold analysis approach
Authors
- Varun Khanna
- Shoba Ranganathan
- Content type: Research article
- Open Access
- Published: 08 August 2011
- Article: 30
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Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision
Authors (first, second and last of 4)
- John D Holliday
- Evangelos Kanoulas
- Peter Willett
- Content type: Research article
- Open Access
- Published: 08 August 2011
- Article: 29
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AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment
Authors (first, second and last of 4)
- Jonna C Stålring
- Lars A Carlsson
- Scott Boyer
- Content type: Software
- Open Access
- Published: 28 July 2011
- Article: 28
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Theoretical NMR correlations based Structure Discussion
Authors
- Jochen Junker
- Content type: Preliminary communication
- Open Access
- Published: 28 July 2011
- Article: 27
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PubChem3D: Biologically relevant 3-D similarity
Authors
- Sunghwan Kim
- Evan E Bolton
- Stephen H Bryant
- Content type: Research article
- Open Access
- Published: 22 July 2011
- Article: 26
This is part of 1 collection: -
PubChem3D: Shape compatibility filtering using molecular shape quadrupoles
Authors
- Sunghwan Kim
- Evan E Bolton
- Stephen H Bryant
- Content type: Research article
- Open Access
- Published: 20 July 2011
- Article: 25
This is part of 1 collection: -
Data governance in predictive toxicology: A review
Authors (first, second and last of 5)
- Xin Fu
- Anna Wojak
- Kim Travis
- Content type: Review
- Open Access
- Published: 13 July 2011
- Article: 24
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4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening
Authors (first, second and last of 4)
- Andreas Jahn
- Lars Rosenbaum
- Andreas Zell
- Content type: Research article
- Open Access
- Published: 06 July 2011
- Article: 23
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Predicting a small molecule-kinase interaction map: A machine learning approach
Authors
- Fabian Buchwald
- Lothar Richter
- Stefan Kramer
- Content type: Research article
- Open Access
- Published: 27 June 2011
- Article: 22
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Consistent two-dimensional visualization of protein-ligand complex series
Authors
- Katrin Stierand
- Matthias Rarey
- Content type: Research article
- Open Access
- Published: 24 June 2011
- Article: 21
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Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration
Authors
- Leonid L Chepelev
- Michel Dumontier
- Content type: Methodology
- Open Access
- Published: 19 May 2011
- Article: 20
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Linked open drug data for pharmaceutical research and development
Authors (first, second and last of 11)
- Matthias Samwald
- Anja Jentzsch
- Susie Stephens
- Content type: Preliminary communication
- Open Access
- Published: 16 May 2011
- Article: 19
This is part of 1 collection: -
AMBIT RESTful web services: an implementation of the OpenTox application programming interface
Authors
- Nina Jeliazkova
- Vedrin Jeliazkov
- Content type: Software
- Open Access
- Published: 16 May 2011
- Article: 18
This is part of 1 collection: -
ChemicalTagger: A tool for semantic text-mining in chemistry
Authors (first, second and last of 4)
- Lezan Hawizy
- David M Jessop
- Peter Murray-Rust
- Content type: Research article
- Open Access
- Published: 16 May 2011
- Article: 17
This is part of 1 collection: -
Semantic Web integration of Cheminformatics resources with the SADI framework
Authors
- Leonid L Chepelev
- Michel Dumontier
- Content type: Methodology
- Open Access
- Published: 16 May 2011
- Article: 16
This is part of 1 collection: -
Resource description framework technologies in chemistry
Authors
- Egon L Willighagen
- Martin P Brändle
- Content type: Editorial
- Open Access
- Published: 13 May 2011
- Article: 15
This is part of 1 collection: -
Analysis of in vitrobioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds
Authors (first, second and last of 4)
- Christopher Southan
- Kiran Boppana
- Sorel Muresan
- Content type: Research article
- Open Access
- Published: 13 May 2011
- Article: 14
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PubChem3D: Similar conformers
Authors
- Evan E Bolton
- Sunghwan Kim
- Stephen H Bryant
- Content type: Research article
- Open Access
- Published: 09 May 2011
- Article: 13
This is part of 1 collection: -
Multilevel Parallelization of AutoDock 4.2
Authors (first, second and last of 5)
- Andrew P Norgan
- Paul K Coffman
- Carlos P Sosa
- Content type: Software
- Open Access
- Published: 28 April 2011
- Article: 12
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Interpreting linear support vector machine models with heat map molecule coloring
Authors (first, second and last of 4)
- Lars Rosenbaum
- Georg Hinselmann
- Andreas Zell
- Content type: Research article
- Open Access
- Published: 25 March 2011
- Article: 11
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Review of "Data Analysis with Open Source Tools" by Philipp K Janert
Authors
- Noel M O'Boyle
- Content type: Book report
- Open Access
- Published: 24 March 2011
- Article: 10
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PubChem3D: Diversity of shape
Authors
- Evan E Bolton
- Sunghwan Kim
- Stephen H Bryant
- Content type: Research article
- Open Access
- Published: 21 March 2011
- Article: 9
This is part of 1 collection: -
Confab - Systematic generation of diverse low-energy conformers
Authors (first, second and last of 5)
- Noel M O'Boyle
- Tim Vandermeersch
- Geoffrey R Hutchison
- Content type: Software
- Open Access
- Published: 16 March 2011
- Article: 8
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Use of structure-activity landscape index curves and curve integrals to evaluate the performance of multiple machine learning prediction models
Authors (first, second and last of 4)
- Norman C LeDonne Jr
- Kevin Rissolo
- Leonard Tini
- Content type: Research article
- Open Access
- Published: 07 February 2011
- Article: 7
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FlaME: Flash Molecular Editor - a 2D structure input tool for the web
Authors
- Pavel Dallakian
- Norbert Haider
- Content type: Software
- Open Access
- Published: 01 February 2011
- Article: 6
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Modular Chemical Descriptor Language (MCDL): Stereochemical modules
Authors (first, second and last of 4)
- Andrei A Gakh
- Michael N Burnett
- Alexander V Yarkov
- Content type: Methodology
- Open Access
- Published: 31 January 2011
- Article: 5