Volume 5, issue 1, December 2013
52 articles in this issue
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CVDHD: a cardiovascular disease herbal database for drug discovery and network pharmacology
Authors (first, second and last of 5)
- Jiangyong Gu
- Yuanshen Gui
- Xiaojie Xu
- Content type: Database
- Open Access
- Published: 18 December 2013
- Article: 51
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Improving structural similarity based virtual screening using background knowledge
Authors
- Tobias Girschick
- Lucia Puchbauer
- Stefan Kramer
- Content type: Research article
- Open Access
- Published: 16 December 2013
- Article: 50
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Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases
Authors (first, second and last of 5)
- Shardul Paricharak
- Tom Klenka
- Andreas Bender
- Content type: Research article
- Open Access
- Published: 13 December 2013
- Article: 49
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Molecule database framework: a framework for creating database applications with chemical structure search capability
Authors
- Joos Kiener
- Content type: Software
- Open Access
- Published: 11 December 2013
- Article: 48
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Complementary PLS and KNN algorithms for improved 3D-QSDAR consensus modeling of AhR binding
Authors (first, second and last of 5)
- Svetoslav H Slavov
- Bruce A Pearce
- Richard D Beger
- Content type: Research article
- Open Access
- Published: 21 November 2013
- Article: 47
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CH5M3D: an HTML5 program for creating 3D molecular structures
Authors
- Clarke W Earley
- Content type: Software
- Open Access
- Published: 18 November 2013
- Article: 46
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International chemical identifier for reactions (RInChI)
Authors
- Guenter Grethe
- Jonathan M Goodman
- Chad HG Allen
- Content type: Research article
- Open Access
- Published: 24 October 2013
- Article: 45
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Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
Authors (first, second and last of 4)
- Gus R Rosania
- Kerby Shedden
- Xinyuan Zhang
- Content type: Methodology
- Open Access
- Published: 05 October 2013
- Article: 44
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Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods
Authors
- Sereina Riniker
- Gregory A Landrum
- Content type: Software
- Open Access
- Published: 24 September 2013
- Article: 43
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Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets
Authors (first, second and last of 8)
- Gerard JP van Westen
- Remco F Swier
- Andreas Bender
- Content type: Research article
- Open Access
- Published: 24 September 2013
- Article: 42
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Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets
Authors (first, second and last of 6)
- Gerard JP van Westen
- Remco F Swier
- Andreas Bender
- Content type: Research article
- Open Access
- Published: 23 September 2013
- Article: 41
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LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions
Authors
- Ségolène Caboche
- Content type: Software
- Open Access
- Published: 29 August 2013
- Article: 40
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MOLE 2.0: advanced approach for analysis of biomacromolecular channels
Authors (first, second and last of 9)
- David Sehnal
- Radka Svobodová Vařeková
- Jaroslav Koča
- Content type: Software
- Open Access
- Published: 16 August 2013
- Article: 39
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MONA – Interactive manipulation of molecule collections
Authors (first, second and last of 5)
- Matthias Hilbig
- Sascha Urbaczek
- Matthias Rarey
- Content type: Research article
- Open Access
- Published: 28 August 2013
- Article: 38
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Full “Laplacianised” posterior naive Bayesian algorithm
Authors
- Hamse Y Mussa
- John BO Mitchell
- Robert C Glen
- Content type: Research article
- Open Access
- Published: 23 August 2013
- Article: 37
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The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites
Authors (first, second and last of 10)
- Adrià Cereto-Massagué
- María José Ojeda
- Gerard Pujadas
- Content type: Software
- Open Access
- Published: 29 July 2013
- Article: 36
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Rubabel: wrapping open Babel with Ruby
Authors (first, second and last of 4)
- Rob Smith
- Ryan Williamson
- John T Prince
- Content type: Software
- Open Access
- Published: 24 July 2013
- Article: 35
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A big data approach to the ultra-fast prediction of DFT-calculated bond energies
Authors
- Xiaohui Qu
- Diogo ARS Latino
- Joao Aires-de-Sousa
- Content type: Research article
- Open Access
- Published: 12 July 2013
- Article: 34
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Inferring multi-target QSAR models with taxonomy-based multi-task learning
Authors (first, second and last of 5)
- Lars Rosenbaum
- Alexander Dörr
- Andreas Zell
- Content type: Research article
- Open Access
- Published: 11 July 2013
- Article: 33
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Cheminformatics for the masses: a chance to increase educational opportunities for the next generation of cheminformaticians
Authors
- David J Wild
- Content type: Editorial
- Open Access
- Published: 05 July 2013
- Article: 32
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Predicting the protein targets for athletic performance-enhancing substances
Authors
- Lazaros Mavridis
- John BO Mitchell
- Content type: Research article
- Open Access
- Published: 25 June 2013
- Article: 31
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Drug repositioning: a machine-learning approach through data integration
Authors (first, second and last of 7)
- Francesco Napolitano
- Yan Zhao
- Dario Greco
- Content type: Research article
- Open Access
- Published: 22 June 2013
- Article: 30
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Review of “Contemporary computer-assisted approaches to molecular structure elucidation (new developments in NMR)” by Mikhail E Elyashberg, Antony Williams and Kirill Blinov
Authors
- Christoph Steinbeck
- Content type: Book report
- Open Access
- Published: 03 June 2013
- Article: 29
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HIM-herbal ingredients in-vivo metabolism database
Authors (first, second and last of 10)
- Hong Kang
- Kailin Tang
- Zhiwei Cao
- Content type: Database
- Open Access
- Published: 31 May 2013
- Article: 28
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Defining a novel k-nearest neighbours approach to assess the applicability domain of a QSAR model for reliable predictions
Authors (first, second and last of 4)
- Faizan Sahigara
- Davide Ballabio
- Viviana Consonni
- Content type: Research article
- Open Access
- Published: 30 May 2013
- Article: 27
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Open-source platform to benchmark fingerprints for ligand-based virtual screening
Authors
- Sereina Riniker
- Gregory A Landrum
- Content type: Research article
- Open Access
- Published: 30 May 2013
- Article: 26
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From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language
Authors
- Wibe A de Jong
- Andrew M Walker
- Marcus D Hanwell
- Content type: Research article
- Open Access
- Published: 24 May 2013
- Article: 25
This is part of 1 collection: -
JSME: a free molecule editor in JavaScript
Authors
- Bruno Bienfait
- Peter Ertl
- Content type: Software
- Open Access
- Published: 21 May 2013
- Article: 24
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The ChEMBL database as linked open data
Authors (first, second and last of 9)
- Egon L Willighagen
- Andra Waagmeester
- David J Wild
- Content type: Methodology
- Open Access
- Published: 08 May 2013
- Article: 23
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In-silico design of computational nucleic acids for molecular information processing
Authors
- Effirul Ikhwan Ramlan
- Klaus-Peter Zauner
- Content type: Research article
- Open Access
- Published: 07 May 2013
- Article: 22
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A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding
Authors
- Ying-Ting Lin
- Content type: Research article
- Open Access
- Published: 30 April 2013
- Article: 21
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Extracting and connecting chemical structures from text sources using chemicalize.org
Authors
- Christopher Southan
- Andras Stracz
- Content type: Software
- Open Access
- Published: 23 April 2013
- Article: 20
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Druggable chemical space and enumerative combinatorics
Authors
- Melvin J Yu
- Content type: Research article
- Open Access
- Published: 18 April 2013
- Article: 19
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Predicting pK a values from EEM atomic charges
Authors (first, second and last of 8)
- Radka Svobodová Vařeková
- Stanislav Geidl
- Jaroslav Koča
- Content type: Research article
- Open Access
- Published: 10 April 2013
- Article: 18
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The influence of the inactives subset generation on the performance of machine learning methods
Authors
- Sabina Smusz
- Rafał Kurczab
- Andrzej J Bojarski
- Content type: Research article
- Open Access
- Published: 05 April 2013
- Article: 17
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Using Pareto points for model identification in predictive toxicology
Authors
- Anna Palczewska
- Daniel Neagu
- Mick Ridley
- Content type: Research article
- Open Access
- Published: 22 March 2013
- Article: 16
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Mining basic active structures from a large-scale database
Authors
- Naoto Takada
- Norihito Ohmori
- Takashi Okada
- Content type: Research article
- Open Access
- Published: 16 March 2013
- Article: 15
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Applications of the InChI in cheminformatics with the CDK and Bioclipse
Authors (first, second and last of 4)
- Ola Spjuth
- Arvid Berg
- Egon L Willighagen
- Content type: Software
- Open Access
- Published: 13 March 2013
- Article: 14
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TB Mobile: a mobile app for anti-tuberculosis molecules with known targets
Authors
- Sean Ekins
- Alex M Clark
- Malabika Sarker
- Content type: Research article
- Open Access
- Published: 06 March 2013
- Article: 13
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Computational mass spectrometry for small molecules
Authors
- Kerstin Scheubert
- Franziska Hufsky
- Sebastian Böcker
- Content type: Review
- Open Access
- Published: 01 March 2013
- Article: 12
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Dragon exploration system on marine sponge compounds interactions
Authors (first, second and last of 4)
- Sunil Sagar
- Mandeep Kaur
- Vladimir B Bajic
- Content type: Database
- Open Access
- Published: 16 February 2013
- Article: 11
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InChI in the wild: an assessment of InChIKey searching in Google
Authors
- Christopher Southan
- Content type: Review
- Open Access
- Published: 11 February 2013
- Article: 10
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Random forests for feature selection in QSPR Models - an application for predicting standard enthalpy of formation of hydrocarbons
Authors
- Ana L Teixeira
- João P Leal
- Andre O Falcao
- Content type: Research article
- Open Access
- Published: 11 February 2013
- Article: 9
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New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms
Authors
- Hwanho Choi
- Hongsuk Kang
- Hwangseo Park
- Content type: Research article
- Open Access
- Published: 04 February 2013
- Article: 8
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InChI - the worldwide chemical structure identifier standard
Authors (first, second and last of 5)
- Stephen Heller
- Alan McNaught
- Igor Pletnev
- Content type: Review
- Open Access
- Published: 24 January 2013
- Article: 7
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Chemical datuments as scientific enablers
Authors
- Henry S Rzepa
- Content type: Commentary
- Open Access
- Published: 23 January 2013
- Article: 6
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Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines
Authors (first, second and last of 8)
- Sheng Tian
- Youyong Li
- Tingjun Hou
- Content type: Research article
- Open Access
- Published: 21 January 2013
- Article: 5
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Modeling of non-additive mixture properties using the Online CHEmical database and Modeling environment (OCHEM)
Authors
- Ioana Oprisiu
- Sergii Novotarskyi
- Igor V Tetko
- Content type: Software
- Open Access
- Published: 15 January 2013
- Article: 4
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UniChem: a unified chemical structure cross-referencing and identifier tracking system
Authors (first, second and last of 10)
- Jon Chambers
- Mark Davies
- John P Overington
- Content type: Database
- Open Access
- Published: 14 January 2013
- Article: 3
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