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ChemSpider – Does Community Engagement work to Build a Quality Online Resource for Chemists?

This is my presentation at the Skolnik Symposium at ACS Denver to honor the contributions of Alexander “Sandy” Lawson to our domain of Cheminformatics.

ChemSpider – Does Community Engagement work to Build a Quality Online Resource for Chemists?

With an intention to provide a high quality free internet resource of chemistry related data for the community, ChemSpider has aggregated almost 25 million compounds linked out to over 400 data sources and provided a platform for the community to both deposit and curate data. This experiment in crowdsourcing for chemistry has now been running for over three years. This presentation will review a number of aspects of the project including (a) the level of community participation in depositing and curating data; (b) the nature of data and content supplied by the community; (c) how ChemSpider is used by the community; (d) using game-based systems to assist in data curation; (e) algorithmic-based approaches to data validation and filtering; and (f) sharing data curation efforts with other online databases.

 

 
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Posted by on August 30, 2011 in Publications and Presentations

 

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Three Articles Published Online in One Week

During my career I have had the opportunity to work with some of the best scientists. During my >10 year tenure at ACD/Labs I directly managed the NMR product line for a number of years and was involved with the development of both the NMR prediction and Computer Assisted Structure Elucidation software. Over the past couple of years since leaving ACD/Labs I have continued to co-author articles with two of my ex-colleagues, and still friends, Kirill Blinov and Mikhail Elyashberg. Three of these articles were released in one work. If you are interested in NMR prediction and CASE systems you might find these articles interesting.

The application of empirical methods of 13C NMR chemical shift prediction as a filter for determining possible relative stereochemistry

Mikhail E. Elyashberg, Kirill A. Blinov, Antony J. Williams
Published Online: Feb 10 2009 8:59AM

DOI: 10.1002/mrc.2396

The reliable determination of stereocenters contained within chemical structures usually requires utilization of NMR data, chemical derivatization, molecular modeling, quantum-mechanical calculations and, if available, X-ray analysis. In this article we show that the number of stereoisomers which need to be thoroughly verified can be significantly reduced using NMR chemical shift calculations for the full stereoisomer set of possibilities using a fragmental approach based on HOSE codes. The applicability of this suggested method is illustrated using a series of complex chemical structures.

A systematic approach for the generation and verification of structural hypotheses

Mikhail Elyashberg, Kirill Blinov, Antony Williams
Published Online: Feb 5 2009 4:33AM

DOI: 10.1002/mrc.2397

In this article we show that the most rational manner by which to create structural hypotheses is by the application of an expert system capable of deducing all potential structures consistent with the experimental spectral data. Empirical or quantum-mechanical (QM) NMR prediction methods are compared. It is shown that when an expert system is used the best structure(s) can be distinguished using either incremental or neural net (NN)-based NMR prediction algorithms.

Development of a fast and accurate method of 13C NMR chemical shift prediction

Available online 11 February 2009
Kirill A. Blinov, Yegor D. Smurnyy, Tatiana S. Churanova, Mikhail E. Elyashberg, Antony J. Williams

DOI:10.1016/j.chemolab.2009.01.010

In this article we describe a fast and accurate method of 13C NMR chemical shift prediction. The high speed of chemical shift calculation described is achieved using a simple structure description scheme based on individual atoms rather than functional groups. The systematic choice of an appropriate encoding scheme and the usage of partial least squares regression on a large training set has resulted in a robust and fast algorithm. The approach provides accuracy comparable with other well known approaches but demonstrates accelerated calculation speeds of up to a thousand times faster.

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Posted by on February 27, 2009 in Uncategorized

 

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ACD/Labs and Pharma Algorithms Join Forces

An announcement today from the company where I spent 10 years of my career, the last few as their Chief Science Officer.

Toronto, Canada (February 9, 2009)—Advanced Chemistry Development, Inc., (ACD/Labs) and Pharma Algorithms, Inc., have joined software development and business resources to better serve the extensive Chemical, Environmental, and Pharmaceutical markets, creating a new leader in in silico physicochemical, ADME, Metabolism, and Toxicology screening and prediction.” More here…

I know the experts from both companies who have been developing the physicochemical property prediction software for many years and this combination of knowledge and expertise in this area is going to be hard to beat now. It will be very interesting to watch what the joint efforts will deliver now.

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Posted by on February 9, 2009 in Uncategorized

 

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