Excuse the silence of late regarding this blog. There has been, and continues to be, a lot of work going on in preparation of a rollout of a new look and feel ChemSpider, hopefully to coincide with our anniversary roll out at Spring ACS in Chicago last year. Fingers crossed we will lift the beta label next week for New Orleans.

In celebration (it’s all serendipity actually!) I will be giving a talk on Sunday in New Orleans, coincident with the day we went live. The details and abstract are below (of course…when the abstract was written it was a placeholder..I had no idea what would be presented because we didn’t know where we’d be)

PAPER ID: 1168843
PAPER TITLE: “ChemSpider: Building a structure-centric community for chemists”

DIVISION: Division of Chemical Information
SESSION: Cheminformatics: From Teaching to Research SESSION START TIME: Sunday, April 6, 2008, 1:40 PM
DAY & TIME OF PRESENTATION: Sunday, April 6, 2008 from 3:40 PM to 4:05 PM
LOCATION: Marriott Convention Center, Room: Blaine Kern D

ChemSpider – Building a Structure Centric Community for Chemists

Antony J. Williams

Scientists commonly find themselves in a state of overwhelm in regards to the availability of information accessible to them. The distribution of resources now includes the entire space of the worldwide web, access to primary databases such as CAS and, commonly, a plethora of internally developed systems. While the web has provided improved access to chemistry-related information there has not been an online central resource allowing integrated chemical structure-searching of chemistry databases, chemistry articles, patents and web pages such as blogs and wikis. ChemSpider has built a structure centric community for chemists by providing free access to an online database and collaboration tool for chemists. The online database offers an environment for curating the data on ChemSpider as well as the deposition of chemical structures, analytical data and associated information and provides a significant knowledge base and resource for chemists working in different domains. An overview of present and future capabilities will be given.

On Tuesday I fly off to St Louis to the SBS Meeting presenting on ChemSpider and the ongoing collaborations around NISS/NCSU’s ChemModLab and SimBioSys’ LASSO. My talk is on Thursday morning.

 

How a Structure-Centric Community for Chemists Can Benefit Drug Discovery – Virtual Screening Experiments Utilizing a Publicly Accessible Ligand Database, QSAR Modeling Tools and a Virtual Docking Software Package

 ChemSpider is an online database of over 20 million chemical structures assembled from almost a hundred data sources including chemical and screening library vendors, publicly accessible databases and resources, commercial databases and Open Access literature articles. Such a public resource provides a rich source of ligands for the purpose of virtual screening experiments. These can take many forms. This work will present results from two specific types of studies: 1) Quantitative Structure Activity Relationship (QSAR) based analyses and 2) In-silico docking into protein receptor sites. We will review results from the application of both approaches to a number of specific examples using the software outlined below.

The QSAR analyses utilize the ChemModLab environment which is a free, web-based toolbox for fitting and assessing quantitative structure-activity relationships. Its elements include a cheminformatics front end to supply molecular descriptors, a set of statistical methods for fitting models, and methods for validating the resulting model. Five molecular descriptor sets are used with 16 math modeling methods to give a total of 80 QSAR models. The input is a file of compounds and a text file for biological activity.

The in-silico docking experiments are conducted using a combination QSAR/Docking approach using the SimBioSys eHITS and Lasso software programs. The docking procedure allows for the screening of a complete molecular database to obtain the correct binding poses and estimated binding affinities. The ligand based screening tool utilizes a novel conformation independent 3D QSAR descriptor, ideally suited for scaffold hopping.

If you are interested in what we’re up to and where we’re going I hope we get to meet-up at one of these gatherings!

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