The in-silico tools and resources for a Design-Make-Test paradigm in small molecule chemistry have significantly advanced in the last half decade. We are nearing a point in time where a chemist can design, plan a synthesis and analyze test results for small molecules all within the same platform so that data flow from workflow management to result analysis is seamless. Additionally, we have a large number of SAR and QSAR tools at our disposal for these purposes each with their own level of functionality and unique capabilities, albeit highly specific to small molecules. Where the gap exists, is when that same synthetic chemist lifts-and-shifts their focus from small molecules to biopolymers and expects their workflows to have the same levels of robust support. The issue being that the governing dynamics of that workflow are inherently different. Instead of optimizing for a single structure, a biopolymer synthetic chemist is focusing on anywhere from 10 – 100 individual small molecules, each requiring optimization, but with the sum of the parts always having to be considered. This presentation will address strides made at Merck Research Labs towards creating in-silico tools to address these needs.
Structure and reaction searching is one of Reaxys’ key strengths, which can only be fully exploited with a powerful, yet easy to use structured query editor. This talk will discuss how structure editors have been used in Reaxys and will present the implementation of Marvin JS in the latest version of Reaxys.
Marvin JS is ChemAxon’s chemical editor web component designed for the wider community. It provides a clean, smart user-oriented interface for quick and convenient drawing of chemical structures and reaction/reactions mechanisms in web pages.
This presentation will focus on the newest development and give a short general overview of the use cases it was designed for.
Right at the beginning, we would like to give our audience a general understanding of ChemAxon’s available solutions and tools. Our senior application scientist will briefly introduce all our available software, and she will put them into context very briefly. This way we will demonstrate how our tools connect to each other offering a solution for several problems.
The presentation will be followed by a long break so that you will have an opportunity to dig deeper into the software that caught your attention. The presentation will also introduce the ChemAxon attendees to look for in the break. At the demo stations, you can try the presented tools, and as always your feedback is deeply appreciated.
This presentation will focus on several, smaller user stories where the core problem is to find relevant chemical data in various internal and external document repositories. The problem gets even more complicated with the different environments our users need to handle.
Some of the data sits on local machines’ drives, but many colleagues used Dropbox or Google folders to store data. Our new ChemLocator tool will be of a great help in these cases.
We will dive deep into five Compound Registration-related topics that are less known, yet interesting to the audience. ChemAxon’s Compound Registration is a system built on a set of web services, aiding users to register molecular structures into a compound database. The registration process spots unique compounds among a set of structures already contained within the database.
The configurability of the registration’s business rules enables flexible definition of uniqueness in accordance with enterprise level requirements. Incoming compound submissions are processed by these business rules, and fully audited registration data is stored for all unique compounds while minimizing the amount of manual curation.
Compliance Checker is a combined software system and content package providing a way to check whether your compounds are controlled according to the laws of the countries of interest.
This presentation shows how chemists and administrators can use the browser-based user interface, and how the RESTful web service API can be used for integration into corporate systems.
Instant JChem is a desktop application designed for researchers and can be considered as a predecessor of the emerging Plexus Suite. Instant JChem allows you to create, explore, and share chemical and nonchemical data in local and remote databases without additional administration. Instant JChem has a wide and growing range of functionality including customizable database views, integration of library enumeration and dynamic population of columns with singular and combined molecular property and descriptor predictions.
Plexus Suite is a web-based software package that accesses, displays, searches and analyzes scientific data. Several ChemAxon tools are integrated into the software suite (with additional tools to come) combining our strong chemistry knowledge with all the technical benefits of a browser-based environment. Plexus Suite consists of various tools. Each tool adds specific knowledge to the major display and query tool – Plexus Connect. Currently, three Plexus Suite tools have been released: Plexus Connect, Plexus Design and Plexus Analysis which can be accompanied by other ChemAxon products.
ChemAxon’s consultancy service help clients: evaluate, deploy, adopt, and extend the utility of our informatics within their research processes and internal workflow systems.
This presentation will very briefly give an overview of the scope of the consultancy team. After the introduction, we will focus more on use cases.
ChemAxon’s Biomolecule Toolkit – now extended with an editor, called BioEddie – is a web service-based toolkit to bridge the gap between biology and chemistry for complex biomolecular entities. It provides unambiguous representation at sequence and atomic level for a diverse set of biomolecules such as peptides, oligonucleotides, proteins, antibody drug conjugates, including those containing unnatural and chemically-modified components; thereby allowing their storage, indexing and search within a database.
The toolkit can be applied to extend existing biologics management platforms or to form the basis of a biomolecule registration system. It is capable of mapping specific workflows and business logic for canonicalization, registration and querying.
Biologics research and development is a complex and lengthy process. Many diverse needs are currently satisfied by a variety of tools with nothing to tie them together. Organizations gravitate towards biologics registration, but this means different things to different users.
In this talk, we will discuss how IDBS are leveraging ChemAxon tools to extend capabilities in biologics research and development.
ChemAxon’s search and database technology includes our JChem Base tool and two cartridges: One running on Oracle, and the other on PostgreSQL. We usually refer to these products as the heart of ChemAxon, since all the search capabilities derive from these tools throughout our software portfolio.
This talk will focus on the latest improvements in JChem PostgreSQL Cartridge.
A publicly accessible web site such as emolecules.com, which offers free searching of over ten million commercially available chemical compounds, presents unique technical challenges to Relational Database (RDB) technology. RDB systems have unpredictable (and often long) search times, poor support for pagination, no feedback on search progress, no support for incremental refinement of search results, and poor support for interrupt/cancel operations. In addition, text-search engines such as Google and Bing have acclimatized users to nearly instantaneous responses, further “raising the bar” of user expectations for a chemical-search web site. Due to these limitations, in 2005 eMolecules developed a custom non-relational cheminformatics search engine that operates in conjunction with an RDB system to meet our customers’ needs via a web-based user interface.
Recent improvements in cheminformatics and relational technology have made it feasible to use ChemAxon’s JChem-PSQL “cartridge,” fully embedded in a Postgres RDB system, for the eMolecules website. In this talk, we outline the challenges and solutions involved in adapting and revising eMolecules’ technology to this RDB system. The result is a web-based chemical search system that provides nearly instantaneous responses, efficient pagination, progress feedback, incremental refinement of search results, and an interrupt/cancel feature.
MadFast is a new innovative product for blazing fast in-memory similarity searches of large chemical sets – processing compound sets with hundreds of millions of sizes.
This presentation will walk viewers through the steps required to get familiar with the three different channels of the tool: its command line interface, the web user interface (UI), and the REST API.
A real-world use case will be demonstrated: a simple similarity-based overlap assessment of molecule sets:
– Import the structures
– Execute exhaustive similarity searches
– Interpret and visualize the results