Cheminformatics tools

The ISIS family of products includes:. JChem is a package that contains Java applications and software development tools for chemistry. JChem Base provides chemical database searching capabilities by integration into relational database engines supporting SQL.

Modules include:. The program uses a knowledge base of transformations to describe generic chemical reactions. The anaylsis of the compounds can be directed by the use of user-definable strategies and tactics. The program can also suggest an appropriate strategy based on its perception of the molecule.

For futher information contact:. Meylan and P. Has been replaced by the ISIS system. A mainframe application used to build, maintain, and search a company's proprietary and commercial databases of 2D and 3D chemical structures and associated research data stored in relational databases.

MDL offers a range of databases that together form an electronic library, giving chemists structure-searchable access to data selectively abstracted from over chemistry journals, chemical supplier catalogs, pharmaceutical patent reports, company reports, regulatory reports, and conference proceedings. The databases -- updated annually, semiannually, or monthly -- cover synthetic methodology, metabolic transformations, 3D structures and data, available chemicals, and bioactivity information.

The OHS Safety Series provides the most comprehensive, independently researched chemical handling and safety information available.

The suite of products and services help organizations manage and make accessible material safety data on over , chemical products selected from the inventories of leading companies. Marvin Applets and Marvin Beans 3. The packages contain software development tools and applications for chemistry. The following are freely available:. Important changes:. Online access also is available for Applets and Applications.

Merlin provides the ability to perform extremely fast searches on selected data in Thor chemical information databases. Merlin operates on sets of structures and is ideal for exploratory data analysis. Merlin is available from Daylight Chemical Information Systems. METEOR originally resulted from a three year research project to develop a computer system for the intelligent prediction of the metabolic fate of xenobiotic chemicals.

The software is continually developed alongside experts from various industry and academic sectors, with knowledge of biotransformations covering phase I and phase II metabolism. The software predicts the metabolic fate of a parent compound, and it also evaluates the likelihood that each predicted metabolite could be found in vivo.

This evaluation considers physicochemical parameters, such as logP. Metabolites can be restricted to those most likely to be of interest by user defined controls.

These include:. The report for a query compound contains specific literature references, and links to external commercial metabolism databases are available. OPTIMA inter-connects the many disparate sources of information about every available substance and reagent. Robotics and automated compound warehouses may also be integrated to provide the complete solution.

This research enterprise solution integrates technology with policy and process considerations to ensure successful deployment. Project Library : A complete, ready-to-use desktop software application for managing project-level combinatorial chemistry data. The system offers user-friendly tools that help researchers create and manage libraries of generic and specific structures, along with associated bioassay, physical, and administrative data. Project Library expedites planning by offering a way to generate virtual libraries and, in conjunction with ISIS and MDL's databases, manages each step of the combinatorial chemistry workflow -- from synthesis planning, through library building and compound screening, to data analysis.

A mainframe application used to build, maintain, and search a company's proprietary and commercial databases of chemical reactions and related data. The product has been replaced and is no longer available. The program is available from Accelrys. This causes small differences in how the libraries treat conditions like aromaticity. I have more experience with the OEChem way and can explain it better. I've developed a set of Python tools to work with molecular fingerprints. I'll describe how to use them to generate fingerprints and do Tanimoto searches.

PyMol is a very popular structure visualization program from DeLano Scientific. It contains an extensive Python programming interface which can be used for structure analysis, movie making, and more.

I'll show you some of the things you can do with it. Many chemistry programs are only available through the command line. I'll show how to use Python's subprocess module to call them from Python. A lot of data is available through web pages designed for people, not software. BeautifulSoup makes it easier to get access to that data in your programs. One example I can cover is how to get data from a PubChem web page. Corporate compound databases are often stored in a relational database like Oracle.

You don't need to be corporate IS to set up a relational database. MySQL is a widely used free database server. I'll shows some examples of creating a database schema, loading compound data into the database, and searching the data set. I've developed a set of chemistry extensions to MySQL so you can get some experience in doing chemically-aware queries, like substructure searches and similarity ranking.

Django is a popular web development framework for Python which makes developing web applications much simpler than traditional CGI programming. These lectures will be based around developing a web application for substructure searches and will cover how to work with the database, generate templates, structure the URLs, using CSS, and Javascript interactivity with JQuery. Software development is more than sitting down and programming. How do you keep track of changes to the code over time?

If you change code, how do you figure out if the change broke something? How to multiple people work together on the same code base? What are some of the common development traps that people can get stuck in? Why do you need to care about security? Many of these are covered in Greg Wilson's Software Carpentry. I'll specifically talk about version control, project builds, testing with nose and development practices like code reviews, YAGNI and agile development.

Despite the best efforts of some, there's still very little direct influence of XML in computational chemistry. But there is sometimes a need, especially when getting data from IT-oriented software developers. Python for Windows has excellent support for COM , which is how Windows programs can embed or control other Windows programs. Chemists use Excel a lot.

Keywords: chemical biology; chemical genetics; chemical library; cheminformatics; drug discovery; drug repurposing; kinase inhibitors; machine learning; mechanism of action; small molecule. Published by Elsevier Ltd.. Candidate preferences are the decision of the Employer or Recruiting Agent, and are controlled by them alone.

To lead this exploration, ROME has assembled a team of world-class leaders across fields including oncology, immunology, virology and machine learning. For more information, please visit. This role will enable project advancement through cheminformatic tools, database administration and data curation with the goal of impacting the efficiency of scientific operations thus enhancing scientific decision-making.

The successful candidate will have experience working on project teams contributing to drug discovery projects using cheminformatics tools, methods and database technologies. Participate in managing outsourced chemistry including compound workflow to bioassays Assist patent counsel and scientific team in patent preparation of experimental methods Help manage and track chemistry contracts with external CROs. Support multi-disciplinary drug discovery and development teams with compound purchasing, registration, shipping, and inventory management.

An understanding of data mining and visualization to contribute to improving ROMEs capabilities in the analysis of structure activity relationships.