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USER MEETING TRANSFORMED: Cheminfo Stories 2020

May 26 – Jun 9, 2020 · #meetCXN

Portfolio Presentation
presentation MarvinSketch Calculator Plugins (logP logD pKa etc...) Marvin JChem Engines Design Hub

This presentation covers the ChemAxon portfolio of products, including recent developments and future directions. Topics include Structure Sketching & Depiction, Chemical Search Engines, Chemical Data Management, Controlled Substance Detection, Chemistry in Documents, Molecular Discovery & Design, Chemistry in Data Worfklows, the Cloud, and Education. It is by no means exhaustive - rather, it is a great way to dip your toe into our many offerings. For an overview of our range of solutions visit our products page.

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Search Engine Improvements
presentation JChem Cartridge JChem PostgreSQL Cartridge JChem Engines JChem Choral Cartridge JChem Microservices

Improvements to ChemAxon's second generation search engine, used in Choral, JChem PostgreSQL and Microservices,in order to serve distributed searches. In this presentation we discuss our roadmap for 2020, and the benefits of distributed searches as well as other improvements.

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AWS Lambdas are Cool
presentation Design Hub

AWS Lambdas are cool for cheminformatics and ChemAxon toolkit usage. In this presentation we discuss 3 main problems that might come up when working with AWS Lambdas.

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Trainable models
presentation Calculator Plugins (logP logD pKa etc...)

This webinar gives insight into recent development of ChemAxon's Calculators and Predictors towards trainable models and new ADMET models. Trainable models give the opportunity to use input data including experimental values and chemical structures to build models automatically using machine learning techniques. The pipeline connects descriptor generation, model building and validation and delivers a model ready to be used. New ADMET models refers to our plans to extend predictions with additional end-points. The talk introduces the first version of the hERG pAct regression model, as the first element in the ADMET group.

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Library Enumeration - The Future of Reactor and Plexus Design
presentation Reactor Plexus Design

The presentation gives a brief summary of our future plans related to the Reactor product family. The first member of our virtual reaction enumeration products was released more than 15 years ago. Since then, this product group has been evolving continuously and boasts several new members including Reactor API, Reactor desktop and command-line application, and Plexus Design. To respond to changing technical needs, emerging large scale reaction enumeration, and multi-step reaction support, we would like to renew this family in the form of the new Library Enumeration.

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Marvin - the next generation of chemical drawing
presentation Marvin

Marvin is a web-based, publication quality chemical editor component which is capable of drawing big synthesis schemes, can be easily extended with other modules, and can be seamlessly integrated in ChemAxon’s products and those of other vendors'. It runs on desktop.

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cHemTS - Harmonized Tariff Schedules with ChemAxon
presentation Compliance Checker cHemTS

This presentation introduces cHemTS, which enables the assignment of tariff codes to organic compounds based on their chemical structure.

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Migration of a central compound management system to state-of-the-art technology
presentation JChem Engines JChem Choral Cartridge

In this talk we describe a recent project with a global pharma company to migrate an existing compound management system to a new system with state-of-the-art technology. The former system was based on BioVia Isentries client with a BioVia direct cartridge. Aim of the project was the migration to a modern web client and a Chemaxon cartridge technology. We used quattro/CM that is tightly coupled to MarvinJS and it can utilize all of the cartridge technologies. The compound management system is not only used for inhouse compounds but also integrate catalog data (ACD, Molport…) with millions of records. This is challenging for complex join queries together with substructure searches. After first development with JChem for Oracle cartridge we migrated to the new Choral cartridge because of better performance on trivial structure searches, that would lead to millions of hits. The integrated relevance ordering of the results together with fast response times are highly suited for hundreds of concurrent users and give convincing results."

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Navigating Massive Virtual (and Real) Libraries
presentation

In recent years, DNA-encoded libraries and reaction based virtual libraries have increasingly been deployed in drug discovery. These vast libraries push the limits of available, readily synthesizable chemical space. So far there are limited solutions to search within these structure sets. Substructure search and similarity analysis are far more challenging when libraries reach very large sizes.  We discuss several technologies to efficiently analyze very large libraries. These tools can help researchers assess the chemical space covered by multiple chemical libraries and aid in hit expansion, scaffold hopping, and idea generation.

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JChem Engines
presentation JChem Base JChem PostgreSQL Cartridge JChem Oracle Cartridge JChem Choral Cartridge JChem Microservices

Overview of different JChem search engines, what are the differences among them, their evolution in the last year. We discuss recent developments on cartridges, retirement of the classic JChem Web Services, and introducing the new JChem Microservices tool. Plans for 2020-2021.

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Leveraging ChemAxon tools to automate Nimbus’ SDFile curation
presentation JChem Engines

As a “virtual” biotechnology company, Nimbus Therapeutics’ operations are entirely enabled through partnering with a wide array of academic and contract research organizations across the globe. Within this model, the coordination of data transfer and integration between multiple partners has historically been a challenge, creating a bottleneck that negatively affected the speed and scalability of the organization. Rebecca Carazza describes in-depth a portion of an automated workflow solution that utilizes ChemAxon technology and KNIME to standardize SDFiles provided to Nimbus through this distributed model. The output is registration ready SDFiles with all required data and formats for database registration.

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JChem for Office News
presentation JChem for Excel JChem for Office JChem for Office Lite

This presentation covers the top 3 news of JChem for Office in 2020 with demo of the most important related features: - JChem for Office Lite is released - Coediting chemical structures and properties in the desktop version of MS Excel - Integration of the BioToolkit into JChem for Excel: Converting HELM to Structure and Structure to HELM

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Impurity Identification Using LC-MS and in silico Reaction Enumeration
presentation Reactor

In this study, we show that using an LC-MS, together with an Excel add-on, named Reactor, impurities can be easily identified at the beginning of the process. Molecular mass values of impurities are detected by LC-MS. Known molecules, like API, known impurities, compounds used during manufacturing etc. can be added to an Excel sheet. Possible reactions, such as dehydration, lactonization, oxidation, adduct formation etc. can also be added to the Excel sheet. Reactor add-on can create reaction products, considering all possible reactants i.e. all known molecules and all possible reactions. Molecular mass values of created (enumerated) products can automatically be compared to measured molecular mass values, which can be a first step to the identification of unknown impurity peaks. These impurities can be submitted for a database search, in order to check their toxicity or genotoxicity.

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A shared Instant JChem database to improve the drug discovery workflow
presentation Instant JChem

Here we will show a typical workflow, issues and solutions put forth for a Medicinal Chemistry project in support of Programs to design small molecules for synthesis.  Typically, in a dynamic biopharmaceutical Research environment, a team of Chemists are assigned chemical entities to design and present why this would be a good candidate for synthesis.  The first problem we see in a manual workflow is that structure ideas presented for next steps can be daunting due to the number of structures that the team will need to assess on a weekly basis.  The meta data information to support a project, like biochemical potencies, chemical properties like clogP, pka, etc. that come with each structure needs to be presented in an efficient manner for the team to review the number of compounds proposed on a weekly basis. The team also needs a platform that is easily incorporated in their workflow to search for compounds that have already been submitted for consideration, for synthesis.  To that end, the Research Informatics team presented the use of ChemAxon’s Instant JChem for managing all newly designed molecules.  This resulted in a cohesive platform wherein all Myokardia ideas are then curated in a client-server system that is backed by an Oracle database for structure/data integrity, security, permissions, indexing and reporting.

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Introducing Design Hub
presentation Marvin Live Design Hub

Our new application has been born out of years of evolution on Marvin Live and a big expansion in 2019, related to hypothesis life-cycle management. We present key capabilities - such as an all new drawing experience, guided molecule design, virtual registration, kanban boards and a universal search engine. We take a thorough look at the various ways the cheminformatics landscape can be tied into Design Hub with the introduction of several classes of new plugins for databases searches (e.g. Enamine REAL) or ADMET property prediction (e.g. the all new ChemAxon hERG predictor). The presentation ends with a look at available cloud subscription plans.

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Instant JChem & Plexus Connect
presentation

Summary of Instant JChem and Plexus Connect's recent advancements. Instant JChem now includes support for the new generation of cartridges, namely JChem PostgreSQL cartridge and Choral. Form editing capabilities were enhanced together with various performance fixes. Plexus Connect begins its new chapter alongside Instant JChem as a web based reporting tool with a completely redesigned UI for more intuitive workflows.

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Exploring Activity Cliffs Using Graph Databases
presentation

Graph databases are becoming increasingly valued in the investigation of highly related datasets. One such example is matched-molecular pairs (MMPs), where the primary point of interest is often a transformation that relates similar structures to one another. This application study examines the use of ChemAxon’s proof-of-concept Neo4j Search Cartridge to represent and investigate MMP databases. Areas of focus include activity cliffs & activity pairs, chemically intelligent node searching and comparing transformations to provide context for activity values, as well as general investigation of the activity landscape.

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ChemAxon Synergy
presentation

This presentation covers 2020 improvements and future plans of ChemAxon Synergy, the evolution of our approach to SaaS solutions for chemistry related R&D data management. The talk gives a brief summary of the fundamental components of such a solution: the capture of chemical data in our Compound Registration tool, the upload of assay results, and the combined visualization and analysis of chemical data and biological results. The visualization component has been replaced with Tableau, building on its strong foundations in visual data analytics. The integration of Tableau into the SaaS solution is presented, with its increased potential using the chemistry extensions developed by ChemAxon. Further active development areas are also discussed, like new compound design – utilizing ChemAxon’s Design Hub application –, along with the handling of laboratory data capture needs.

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A new approach to ELN for the chemical enterprise and ChemAxon solutions for its chemical functionality
presentation

A new unique ELN (electronic laboratory notebook) was developed by Israeli software company Comply and implemented in global R&D of the biggest in the world generic agrochemical company Adama. This ELN may be characterized as electronic laboratory environment (ELE) that support all workflow of the product development in the company. During the presentation different modules of ELE that are using software of ChemAxon were demonstrated. It was shown how chemical structures may be introduced to ELE, used for experiments planning calculations, delivered for report preparation and how structure / substructure search for chemical information in ELE may be executed.

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Chemical intelligence in Tableau
presentation

The possibilities that ChemAxon offers within Tableau: adding the capability to render images dynamicaly, with our developments one may add the visualization of chemical structures to views or dashboards. On top of this, substructure search and similarity search have also been added to the options.

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Introducing Chemlocator
presentation ChemLocator

ChemLocator is useful tool for extracting chemical and biological insights from documents. The count of yearly published articles, patents, journals etc. is wildly increasing. In this presentation we show how the tool will save you time and take some load off your shoulders when your job needs document searching. We show how to use it through its built-in web-based user interface and also introduce the way of API level integration into 3rd party applications.

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Use of ChemAxon Marvin JS and JChem library to support the development of a new web application for iPPI-DB
presentation Marvin JS JChem Engines

Here, we present an updated version of iPPI-DB, our manually curated database of PPI modulators. In this release, the data model, the graphical interface and the tools to query the database have been completely redesigned. We used Chemaxon MarvinJS and JChem library to support this development. We added new PPI modulators, new PPI targets, and extended our focus to stabilizers of PPIs as well. Finally, we introduce a web application relying on crowdsourcing for the maintenance of the database. This application can be used outside of our group to collaboratively maintain iPPI-DB within a community of curators.

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Update on Chemicalize Professional
presentation Chemicalize Pro

Chemicalize is an online SaaS product providing UI based chemical calculations, drawing and searching as well as API based endpoints for integrators and embeddable web components for website owners. In the presentation we introduce the service and showing the essence of the embeddable web components through a real-life use case focusing on the compliance questions.

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Compliance Checker SaaS Subscriptions
presentation Compliance Checker

This presentation introduces the new SaaS Subscription types available for theCompliance Checker Software as a Service solutions.

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Cheminformatics in IP
presentation Markush Editor

The presentation gives a brief overview of the role of Cheminformatics in different fields of IP, and how ChemAxon tools serve these fields. Introducing solutions for indexing chemical information in the patent documents, tools for making the extracted information chemical searchable, and finally, a unique tool for computer added chemical patent drafting. Besides the short introduction of the relevant ChemAxon applications (Document to Structure, ChemLocator, ChemCurator, Markush Editor, JChem) we also discuss the main challenges of the IP from Cheminformatics viewpoint.

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See IP Differently – The power of using visualized intellectual property (IP) strategy and intelligence to guide molecular research and drug discovery
presentation ChemCurator

At a time when the importance of fast and effective drug discovery is at the forefront of so many minds, the need for technology-based tools which can support and improve the efficiency of designing and synthesizing drug candidates has never been greater. Machine learning and AI are being increasingly leveraged as part of the medicinal chemistry process to improve productivity from a chemical perspective, but what about using the legal, licensing and commercial aspects to guide R&D activities? Accencio®’s IP-GeoScape® technology curates vast amounts of molecular information from patent publications using ChemAxon’s ChemCurator tool, and visualizes the mathematical structural relationships between these molecules. Vital scientific and commercial information is strategically layered into the visualizations - enabling faster, more focused and precise R&D efforts.

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IncoPat together with ChemAxon - Your partners on the road of innovation
presentation

incoPat, a patent database vendor from China, has formed a partnership with ChemAxon, as a result of which, incoPat will be able to provide a better service for their clients, especially those from the pharmaceutical industry. Since 2011 the incoPat database has grown into a global collection of patents from 120 countries with integrated functions including patent search, analysis, and monitoring.

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