Chemistry Central Blog
Chempedia: "a free and continuously-updated" chemical compound encyclopaedia
Each compound monograph outlines information about the "structure, uses, history, and significance of a chemical compound". Users can search for compounds through the 'ChemWriter Structure Editor' or by text using a title, CAS Number, or PubChem CID. There is also the option to search the compound listings alphabetically or by most recent items.
The compound entries can be updated as soon as possible to reflect newly available information. Here users are well placed to know when an existing Wikipedia compound monograph ought to appear in Chempedia yet does not, when an existing monograph needs to be updated, or when a new monograph has been written and needs to be linked. All users need to do in order to create a new or updated link from Chempedia to Wikipedia, is to provide the Wikipedia link via the 'create' tab found on the site's main menu.
Posted by Gino D'Oca at 16:18 Comments (0)
New, free-to-access life sciences search engine
A new, free-to-access life sciences search engine has been recently made available to the general public. NextBio allows users to search over 10,000 public experimental results, 1.2 billion data points, and 16 million PubMed literature abstracts, making "massive amounts of disparate biological, clinical and chemical data from public and proprietary sources searchable, regardless of data type and origin....".
The search engine's framework, which connects heterogeneous data and textual information, was previously only provided in an "enterprise version" for life science R&D and drug development, with notable users including Johnson & Johnson Pharmaceutical Research & Development. The "enterprise accounts" differ from the free version in that they include "added data integration services, security and support".
The research areas covered by NextBio's publicly searchable data range from pharmacogenomics to oncology. Functionality exists to allow users to import their own analysed experimental results, where they can choose to share their data with the network or restrict access to a limited audience. Users can also create their own profiles to more easily develop collaborations with other scientists.
NextBio's founders state that it
"...provides a unique opportunity for the research
community to collaborate through information sharing and to perform an important
part of their biological work in silico... [allowing users]... to glean new
insights into gene function, disease progression and compound effects, as well
as into their own studies using the world's quality public experiments..."
There
are plans to incorporate further content into the platform in due course, such as
sequence-centric and phenotypic data types. Helpful and informative video demonstrations can be found on the site, offering an overview of the initiative's "open biology" ethos, as well as a tutorial on how to use the search engine.
Posted by Gino D'Oca at 16:19 Comments (0)
Open database for insect semiochemicals
To continue our theme of providing overviews of free-to-access chemical databases, I feel Pherobase, a interesting database of insect behaviour modifying chemicals, to be well worth a mention.
The database, hosted by the chemical ecology group, HortResearch, New Zealand, is aimed at "convert[ing] scientific data and knowledge from the literature and publish[ing] peer-reviewed information about behavioural modifying chemicals in insects into electronically searchable database entries." Chemical signals are the main channel of communication in arthropods, especially insects, finding uses in, amongst other things, sexual attraction and defence. The project's author believes the database will "...definitely aid and [accelerate] the process of semiochemicals' (Ed: chemical substance that carries a message) identification and... will provide an overview of the hetero-specific overlap in the chemical signals between different animal groups."
The database, which has now grown to over 50,000 entries - of which 3,000 contain details on molecules -, also contains mass spectral data on over 1,500 of the compounds. Users can search by text, or browse a large number of categories, including genus, species, and functional group, but also application, such as 'lure and kill' and 'mating disruption'. In addition to having an interactive Jmol molecular model, each compound page contains links to spectra, as well as references regarding synthesis and behavioural function.
Pherobase is yet another
example of a free-to-access database, which benefits from being enriched and augmented by contributions from
interested specialists, and that in spite of attracting a somewhat
niche audience, nonetheless has high practical utility.
***
On a related note, it is
worth highlighting Anthony Williams' (ChemSpider) review of the
status of public chemical databases that was recently published in BioMed
Central's Current Opinion in Drug Discovery and
Development. The following is an excerpt from the abstract:
“...The increasing array of chemistry-related resources that are now available provides chemists with a direct path to the information that was previously accessed via library services and was limited by commercial and costly resources. The diversity of the information that can be accessed online is expanding at a dramatic rate, and the support for publicly available resources offers significant opportunities in terms of the benefits to science and society. While the data online do not generally meet the quality standards of manually curated sources, there are efforts underway to gather scientists together and 'crowdsource' an improvement in the quality of the available data...” Public chemical compound databases: Current Opinion in Drug Discovery and Development 2008, 11:393-404 (18 April 2008).
Posted by Gino D'Oca at 16:14 Comments (0)
CAS agrees to cooperate with Wikipedia
In a positive turnaround Chemical Abstracts Service (CAS) has announced that it will support the 'CAS Number Validation project' started at Wikipedia Chemistry to assist in producing a curated dataset.
"CAS, a division of the American Chemical Society... will contribute to the Wikipedia project... to help provide accurate CAS Registry Numbers for current substances listed in Wikiprojects-Chemicals... that are of widespread general public interest...". The statement goes on to say that "CAS views Wikipedia as an important societal tool for the general public, and this collaboration with Wikipedia is in line with CAS' mission as a Division of the American Chemical Society."
The declaration comes after CAS had earlier made clear its objection "to anyone encouraging the use of SciFinder and STN to curate third-party databases or chemical substance collections, including the one found in Wikipedia. SciFinder and STN are provided to researchers under formal license agreements, under which the researchers agree to refrain from using these tools to build databases. We urge and expect those researchers to respect the explicit terms of the agreements they have entered into..."
CAS's agreement to
cooperate comes on the back of discussions with Martin Walker of WP:Chem and the ChemSpider
Advisory Group, in addition to much debate that ensued elsewhere.
The aim of the validation project is to address various concerns, which
include CAS numbers not matching the structure drawn in the Wikipedia's 'Chemical
Box' or 'Drug Box'. The import of CAS's cooperation was reiterated on the ChemSpider blog: "...there is general agreement by all participants at WP:Chem
that CAS Numbers have value... so the presence of a CAS number in the
[Wikipedia] boxes makes absolute sense and, of course, the correct CAS number
for the structure makes sense in an encyclopedia."
Posted by Gino D'Oca at 11:18 Comments (0)
Open database for structural biologists
Proteopedia, a new open database for biologists and chemists, has been recently launched. The project's scope is the "[collection and dissemination of] structural biological and biological knowledge about proteins, RNA, DNA, and their assemblies and interacting small molecules in a manner that is... accessible...".
At present the database - which was created in 2007 by Joel Sussman, Eran Hodis and Jaime Prilusky, researchers at The Weizmann Institute of Science, Israel - has around 50,000 searchable entries, including one page for each entry in the Protein Data Bank (PDB). Most of the pages are titled with a four-character PDB identification code, and the database is updated regularly to assimilate new data released by the PDB. In addition to those identified with a PDB code, there are also entries dedicated to particular molecules and topics, such as Glycine, Antibodies and Serine Protease.
The database is another example of numerous new projects whose aim is to provide open data whilst also embracing new technologies for their display. The project's broader three-fold aims are thus:
- To serve as a forum for scientists to share, retrieve and discuss information related to proteins, macromolecules, and small molecules and chemicals of interest.
- To continue to develop the concept of tying text to three-dimensional, interactive images.
- To maintain low barriers for contribution.
Posted by Gino D'Oca at 11:53 Comments (0)
Consolidated Appropriations Act 2008: positive for open access, disappointing for chemistry?
Many of you will by now be aware that in December
the Consolidated Appropriations Act 2008 was signed into US law by President
Bush. This means that the National Institutes of Health's (NIH)
Public Access Policy, which was previously voluntary, is set to become
mandatory, marking a pleasing development for proponents of Open Access. BioMed
Central's Publisher, Matt Cockerill, has already outlined what the policy
means on the BMC blog.
While this is important news to us at Chemistry Central, it is also worth
remembering that this is only a very small part of huge bill, which sets out
federal research and development funding budgets for the coming year.
Overall, total federal investment in research and development is to increase by
1.3% to $142.7 billion. In particular, the NIH's total budget for 2008 will
stand at $29.5 billion (97% of which is R&D spending), a mere increase of
0.9% ($275 million) on last year, and $776 million less than laid out in
November's vetoed appropriation. If enacted, the increase will mark the
fifth consecutive year in which NIH funding has not risen in tune with
'biomedical inflation' (see table A here), which has been
estimated at 3.7%.
Much of the NIH increase is earmarked for the Global Fund to Fight HIV/AIDS,
Tuberculosis, and Malaria, and the NIH Common Fund, meaning that the budgets of
all NIH institutes and centres will remain essentially flat in 2008 (increasing
by around 0.1%), thus also falling well short of THE economy-wide inflationary
increase, which is projected at 2.4%.
What does this mean, specifically, for chemical research?
The research and development budget announcement is a cause for some
concern amongst researchers, a sentiment that has been voiced elsewhere,
notably in relation the potential effects on chemical industry if cuts were made at
the Department of Energy (DOE). In addition
to the NIH, there are numerous other bodies whose budgetary increases are of
particular interest to chemists. Under the appropriation, the National Science
Foundation's research and development investments are to increase to $4.5
billion, marking a 1.1% rise, meaning that in real terms funding will remain below
that of last year. The Environmental Protection Agency, much of
whose research is chemistry-related, will see its Science and Technology
account budget increase by 3.3% to around $760 million; while the Office of
Science, through which much of the DOE's chemistry funding comes, will see an increase of only 5.8% (3.5% in real terms).
A comprehensive summary of all appropriations for R&D and public health
programs can be found here.
Posted by Gino D'Oca at 17:03 Comments (0)
ASSOCIATE PUBLISHER, CHEMISTRY (Ref: BMC/CAP)
Chemistry Central, part of BioMed Central Ltd requires an experienced chemist with publishing experience to develop and expand its new portfolio of chemistry journals.
The role of the Associate Publisher will involve leading the development of the portfolio of open access journals through proactive launches/acquisitions in high growth areas of chemistry, including multidisciplinary research. You will also oversee the editorial process for Chemistry Central Journal and newly launched journals, managing the in-house Assistant Editor(s) and relations with external journal editors, Editorial Advisory Boards (EAB) and authors.
You will represent Chemistry Central at industry events and academic conferences, to promote the journal portfolio, solicit manuscripts, liaise with Editorial Boards and advocate open access in chemistry.
The role will also involve the planning and coordination of appropriate use of web technologies to improve the delivery and linking of chemical information within the journals and with external resources.
A PhD in chemistry or related discipline is essential, as is previous experience of scientific publishing. An understanding of chemistry-related web technologies would be an advantage.
The position will be based in London and will report to the Deputy Publisher, BioMed Central.
Further information can be obtained by contacting Bryan Vickery (bryan<dot>vickery<at>chemistrycentral<dot>com)
Please send your CV and covering letter, stating salary expectations and quoting job reference to: Recruitment, SNG, 34-42 Cleveland Street, London, W1T 4LB, or by email to: jobs@sciencenow.com.
Posted by Bryan Vickery at 16:09 Comments (0)
Chemistry Central Journal publishes new research article
Research article
Characterisation
of temperature-dependent phase transitions in
2,2-trimethylenedioxy-4,4,6,6-tetrachlorocyclotriphosphazene,
N3P3Cl4[O(CH2)3O]
Simon
J Coles, David B Davies, Michael B Hursthouse, Susanne L Huth, Adem
Kilic, Mark E Light, Marianne Odlyha, John S Rutherford, Robert A Shaw,
Aylin Uslu
Chemistry Central Journal 2007, 1:20 (18 July 2007)
[Abstract] [Provisional PDF]
The crystal structure of
2,2-trimethylenedioxy-4,4,6,6-tetrachlorocyclo- triphosphazene has been
determined at 120, 274 and 293 K. The result obtained at 293 K confirms the room
temperature Cmc21 structure, but at the
lower temperatures the space group is Pna21. Nevertheless the basic structure
remains the same, with only small displacements of the atoms, amounting to an
average of 25 pm between 120 and 293 K. The
article outlines how X-ray diffraction and DSC results indicate that the
phase transition takes place in two steps between 274 - 293K providing an
understanding of previous NQR results. In the intermediate temperature range the molecules are displaced
from their room temperature positions in such a way as to give an average
structure with Cmc21 symmetry. The authors conclude that the overall phase
transition is consistent with the occurrence of a soft lattice mode at room
temperature in which a large displacement of the molecule in the x-direction is
coupled with a flexing motion about an axis defined by the nitrogen atoms in the 1 and 5 positions.
Posted by Gino D'Oca at 14:49 Comments (0)
Chemistry Central Journal publishes new commentary article
| Commentary Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions Adrian J Mulholland Chemistry Central Journal 2007, 1:19 (5 July 2007) [Abstract] [Provisional PDF] |
Combined quantum mechanics/molecular mechanics (QM/MM) modelling has the potential to answer fundamental questions about enzyme mechanisms and catalysis. Calculations using QM/MM methods can now predict barriers for enzyme-catalysed reactions with unprecedented, near chemical accuracy, i.e. to within 1 kcal/mol in the best cases. Quantitative predictions from first-principles calculations were only previously possible for very small molecules. At this level, quantitative, reliable predictions can be made about the mechanisms of enzyme-catalysed reactions. This development signals a new era of computational biochemistry.
Posted by Gino D'Oca at 16:57 Comments (0)
Chemrank gives a thumbs-up (or down!) to chemical research
Posted by Gino D'Oca at 13:46 Comments (0)
Chemistry Central Journal publishes commentary article on white biotechnology
| Commentary Relevance of Chemistry to White Biotechnology Munishwar Gupta, Smita Raghava Chemistry Central Journal 2007, 1:17 (20 June 2007) [Abstract] [Provisional PDF] |
Posted by Gino D'Oca at 14:31 Comments (0)
Chemistry Central Journal publishes three new research articles
A multipurpose immobilized biocatalyst with pectinase, xylanase and cellulase activities
Sohel Dalal, Aparna Sharma, Munishwar NATH Gupta
Chemistry Central Journal 2007, 1:16 (8 June 2007)
[Abstract] [Provisional PDF]
Research article
Core charge distribution and self assembly of columnar phases: the case of triphenylenes and azatriphenylenes
Silvia Orlandi, Luca Muccioli, Matteo Ricci, Roberto Berardi, Claudio Zannoni
Chemistry Central Journal 2007, 1:15 (8 June 2007)
[Abstract] [Provisional PDF]
This article looks at the use of computer simulation techniques in investigating the effects on phase behaviour of triphenylenes and azatriphenylenes owing to changes of the charge distribution in the discotic core. In it, the authors conclude that the intermolecular electrostatic potential among the cores is fundamental in stabilizing/destabilizing columnar phases; in particular the triphenylene charge distribution stabilizes the columnar structure, while the azatriphenylene distribution suppresses its formation in favour of the nematic phase. It is envisaged, therefore, that the model could be successfully employed as the basis for coarse-grained level simulations of a wider class of triphenylene derivatives. The article brings new quantitative results to study of structure/properties relationship of discotic molecules and columnar supramolecular organisation.
Research article
Characterization of Italian honeys (Marche Region) on the basis of their mineral content and some typical quality parameters
Marcelo E Conti, Jorge Stripeikis, Luigi Campanella, Domenico Cucina, Mabel B Tudino
Chemistry Central Journal 2007, 1:14 (7 June 2007)
[Abstract] [Provisional PDF]
This article looks at the characterization of three types of Italian honey - Acacia, Multifloral, Honeydew - on the basis of their mineral content and other parameters (pH, sugar content, humidity). Pattern recognition methods such as principal components analysis (PCA) and linear discriminant analysis (LDA) were performed in order to classify the honey samples whose botanical origins were different, and identify the most discriminant parameters. Lastly, using ANOVA and correlations for all parameters, significant differences between diverse types of honey were examined.
Posted by Gino D'Oca at 14:04 Comments (0)
Different extraction methods of biologically active components from Propolis: a preliminary study
Preliminary communication
Different extraction methods of biologically active components from Propolis: a preliminary study
Boryana Trusheva, Dorina Trunkova, Vassya Bankova
Chemistry Central Journal 2007, 1:13 (7 June 2007)
[Abstract] [Provisional PDF]
This short communication compares three techniques (traditional maceration, ultrasound, and microwave assisted extraction) used to extract the biologically active constituents of propolis, a natural product for which there is a high scientific and commercial interest. The authors conclude that, compared to maceration extraction, the other two methods provide higher extraction yield, and require shorter timeframes and less labour, with UE shown to be the overall most efficient method.
Posted by Gino D'Oca at 14:03 Comments (0)
Fast 3D shape screening of large chemical databases through alignment-recycling
| Methodology Fast 3D shape screening of large chemical databases through alignment-recycling Fabien Fontaine, Evan E Bolton, Yulia Borodina, Stephen H Bryant Chemistry Central Journal 2007, 1:12 (6 June 2007) [Abstract] [Provisional PDF] |
A new method for efficiently performing 3D structural searches in a dataset of more than one million PubChem compounds of limited size (<28 heavy atoms) and flexibility (<6 rotatable bonds) is presented. In current 3D search methods, it is necessary to compute the optimal overlay between the query and database molecules to obtain shape similarity values, a necessity that adds a significant amount of overhead to the search time. The alignment-recycling method presented in this article, however, reduces the CPU time required to perform shape similarity searches. The authors also discuss extensions and variations to the methodology, for example, to handle more flexible and larger small-molecules. The article will interest those who are working in the field of 3D molecular alignment and related disciplines.
Posted by Gino D'Oca at 14:02 Comments (0)
Editors' Choice: In-silico docking HIV-1 integrase
"Human immunodeficiency virus (HIV) is a retrovirus that causes acquired immunodeficiency syndrome (AIDS), the World Health Organisation (WHO) estimates that AIDS has killed 25 million people since it was first identified. HIV-integrase is an important new drug target with several clinical trials underway, however, questions remain about the detailed binding interactions, a knowledge of which may be critical in our understanding of drug resistant mutations. The docking studies described in this publication identify possible poses that are consistent with drug resistance profiles, the observed binding affinities and offer further insights into the key binding interactions".
Research
In-Silico docking of HIV-1 integrase inhibitors reveals a novel drug type acting on an enzyme/DNA reaction intermediate
Andrea Savarino
Retrovirology 2007, 4:21 (20 March 2007)
[Abstract] [Provisional PDF]
Posted by Bryan Vickery at 09:52 Comments (0)