Posts tegged as 'cheminformatics'

Solubility prediction - ChemAxon's Solubility Predictor

Aqueous solubility for organic compounds is one of the most important physico-chemical properties in modern drug discovery and has long been among our plans. Being a property that is hard to model, providing a tool for prediction, in a fast and accurate way, has not been an easy task and so we are pleased to announce our solution in the latest 6.3 release.

ChemAxon’s Solubility Predictor is able to predict aqueous intrinsic solubility and pH-solubility profile for molecules. An example below shows the prediction results for the acebutolol molecule.

acebutolol_solubility
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Reconciliation of metabolites and biochemical reactions for metabolic networks

Genome-scale metabolic network reconstructions are now routinely used in the study of metabolic pathways, their evolution and design. The development of such reconstructions involves the integration of information on reactions and metabolites from the scientific literature as well as public databases and existing genome-scale metabolic models. The reconciliation of discrepancies between data from these sources generally requires significant manual curation, which constitutes a major obstacle in efforts to develop and apply genome-scale metabolic network reconstructions. In this work, we discuss some of the major difficulties encountered in the mapping and reconciliation of metabolic resources and review three recent initiatives that aim to accelerate this process, namely BKM-react, MetRxn and MNXref (presented in this article). Each of these resources provides a pre-compiled reconciliation of many of the most commonly used metabolic resources. By reducing the time required for manual curation of metabolite and reaction discrepancies, these resources aim to accelerate the development and application of high-quality genome-scale metabolic network reconstructions and models.

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Challenges of polymer informatics and the driving force

Jul 4, 2013Krisztián Niesz

Polymers are arguably the single most used materials in the modern age, however there are only a small number of useful informatics tools out there to work with polymers. According to expectations the world annual consumption is approaching 400 million metric tons(!) by 2016 (which is up by 70% from 2006), and the market sectors include anything and everything that you can possibly imagine: food, textiles, furniture, printing, plastics, machinery, electronics, transportation, construction, and so on. So, I think it is safe to say that our civilization depends on polymers.

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chemicalize.org's crowdsourced database - now in Pubchem

Jan 23, 2013András Strácz

Over the past few years, one of the most surprising community effects have been playing out on chemicalize.org: building a huge crowdsourced database of interesting chemical structures. How?

Webpage Viewer and Document Viewer, two major services of the free chemicalize.org website save all visited URLs along with the chemical structures found on the page. Perhaps I don’t need to detail how this is done, but it involves things like Document to Structure and being able to understand every chemical format out there.


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Stereo models explained

Stereo models determine the way stereo chemistry is calculated, which affects stereo matching. The differences centre around the issue of symmetry. Our documentation has improved with additional examples and better descriptions yet it seems users can sometimes still be confused. This time we try to illustrate stereo models through three likely conversations we would have when explaining to users. Hope this helps with understanding.

Cast:

  • Poor ChemAxon Developer (PCD)
  • Chemist liking global stereo model (C♥GLOB)
  • Chemist liking comprehensive stereo model (C♥COMP)
  • Chemist liking local stereo model (C♥LOC)

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How could cheminformatics be utilized for greener petrochemical processes?

Dec 13, 2012Krisztián Niesz

Global warming is a major issue and preserving the environment is becoming an enormous challenge, questions arise: How come cheminformatics has not been fully applied to help reseachers in finding less polluting, less toxic chemicals or replacing currently practiced chemical processes which have significant environmental impact? How come cheminformatics in petrochemistry is still in its infancy comparing to pharma where it is a well-established approach, producing a large variety of well-maintained and continuously evolving tools? Even the entry for Wikipedia reflects this bias, defining cheminformatics as in silico techniques that are used in pharmaceutical companies in the process of drug discovery. Does this mean that the two somewhat related fields of chemistry are so different from each other after all that software designed for one cannot be used in the other? And finally there is the title question ‘How could cheminformatics be utilized for greener petrochemical processes?’ seeking an answer.

On the one hand, if we were about to compare the different sectors of chemical business we would see that basic chemicals, which includes bulk petrochemicals, polymers, intermediates, inorganics, fertilizers, etc., are to cover about the same size of market as the pharma sector (35% and 30%, respectively). From this I think we are not far from the truth by concluding that probably both industries would need this computational support equally.

Global business of chemistry by sectors

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Structure visualization - Which are your favourite visualization styles?

Nov 19, 2012Eufrozina Hoffmann

With the upcoming launch of Marvin for JavaScript we wanted to find out what you expect to see when working with a chemical editor.

These seven images, from different chemical editors, represent the structure 2-Chloro-1-(2,4-dichlorophenyl)-3-(1H-imidazol-1-yl)-2-phenylpropan-1-one.

We would like to know which style version you like and why. Please take the survey below (“Start” button) to tell us the which-es, the why’s and why not’s!

Marvin for JavaScript visualization types

(Image credits: Ödön Farkas, Group of ChemoInformatics & Molecular Modeling at Eötvös Loránd University.)

Survey about Marvin for JavaScript

Survey about Marvin for JavaScript

Which are your favourite visualization styles?

Nanotech drugs reach FDA with all the obscurity

Nov 19, 2012Krisztián Niesz

When I was browsing through Chemical & Engineering News recently an article about how the Food & Drug Administration (FDA) struggles to come up with appropriate processes to review new nanotechnology-based drug applications caught my attention, and had me thinking about how/if cheminformatics can be called to help here. According to this discussion “Mapping Nanotech Drug’s Landscape” (requires subscription to read) the FDA sees the main cause of the problem as having inconsistent characterization data from drug manufacturers or even having no data available at all.

Nanomaterials in medical chemistry

Nanotechnology itself has already passed the state of being only a buzzword, and by now has invaded many technological areas providing great benefits for society. Although it is a difficult, possibly overwhelming task to get a track on each commercially used “nano” product, it is believed that there are already 1000’s distributed worldwide, mainly in areas of the electronic, cosmetic, automotive and medical industry and, without doubt, more are yet to come. Read the more »

Convert chemical file formats in Python using JChem Web Services

Nov 19, 2012Gábor Guta

Chemical file formats can always cause trouble, because most of the tools do not support all formats or cannot handle specific formats properly. ChemAxon’s platform provides high quality chemical file format handling, but the library is in Java. We describe how our library can be accessed through Python.

We assume that you are familiar with Python (we assume 3.x, which is backward-incompatible with version 2.x line) to some extent so you would like to develop your solution in this programming language. Installing the JChem Web Services is not a big deal, all you have to do is download it from here and execute the installer (on linux or on mac you have to extract the archive into a folder and start the services with startup.sh in the bin folder).

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Welcome to the Blog!

Nov 19, 2012Alex Allardyce

Welcome, come on in to the ChemAxon Blog!

Why did we start this

We wanted an area separate from the technical support forum where we could talk more generally about chemistry, informatics, what is happening at ChemAxon – future products/features, the changing technology environment and the business of RnD.

What this isn’t

An area for technical support. It would be fine to comment on support materials or discuss feature development more generally but “How do I do this in Marvin?” or “xzy_class is throwing an exception…” are really better served over at the forum (6,000+ topics, 32,000+ posts), not least because the right people are tracking topics over there and also it may already have been answered.

We hope this is interesting and look forward to hearing your point of view.

Alex

ChemAxon Staff&UGM Attendees

P.S.: I add this image – it’s a favorite because there are so many of us in there and I am looking stylish whilst drinking beer. Source: ChemAxon UGM Budapest 2010, Széchenyi Bathouse.