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https://chemaxon.com/hs-fs/hubfs/Hero%20images/Calculations_Discovery-Tools.jpg?width=4098&height=2306&name=Calculations_Discovery-Tools.jpg 4098w, https://chemaxon.com/hs-fs/hubfs/Hero%20images/Calculations_Discovery-Tools.jpg?width=5464&height=3074&name=Calculations_Discovery-Tools.jpg 5464w, https://chemaxon.com/hs-fs/hubfs/Hero%20images/Calculations_Discovery-Tools.jpg?width=6830&height=3843&name=Calculations_Discovery-Tools.jpg 6830w, https://chemaxon.com/hs-fs/hubfs/Hero%20images/Calculations_Discovery-Tools.jpg?width=8196&height=4611&name=Calculations_Discovery-Tools.jpg 8196w" sizes="(max-width: 2732px) 100vw, 2732px"> </div> <div class="VerticalHero__text" style="max-width:680px"> <div class="flow xl-heading"><h1>Discovery Tools</h1> <h2>From clustering and diversity analysis for chemical libraries to 2D and 3D molecular screening</h2></div> </div> </div> </div> </div></div> </div> </div> </div> <div class="row-fluid-wrapper row-depth-1 row-number-3 "> <div class="row-fluid "> <div class="span12 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="0" data-w="12"> <div id="hs_cos_wrapper_widget_1663316404680" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="SectionTitle border "> <div class="SectionTitle--left grid grid-padding "> <div class="SectionTitle__content" style="max-width:680px"> <div class="flow xl-heading"><h2>JKlustor</h2> <p> </p></div> </div> </div> </div></div> </div> </div> </div> <div class="row-fluid-wrapper row-depth-1 row-number-4 "> <div class="row-fluid "> <div class="span2 widget-span widget-type-cell dnd-column" style="" data-widget-type="cell" data-x="0" data-w="2"> <div class="row-fluid-wrapper row-depth-1 row-number-5 "> <div class="row-fluid "> <div class="span12 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="0" data-w="12"> <div id="hs_cos_wrapper_module_1662805591412" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="TwoColumnBanner "> <div class="grid grid--cols-2 grid--align-end"> <div class="TwoColumnBanner__text grid-padding"> <p class="supertitle">JKlustor Summary</p> <div class="flow xl-heading"><h2>JKlustor - Clustering and diversity analysis for chemical libraries</h2> <p>JKlustor is a suite packed with clustering methods, that performs similarity and structure based clustering of compound libraries and focused sets - in both hierarchical and non-hierarchical fashions. The suite also carries out diversity calculations and library comparisons based on molecular fingerprints and other descriptors. It is an essential tool in combinatorial chemistry, virtual library design, and other areas where large numbers of compounds are analyzed.</p></div> </div> <div class=" TwoColumnBanner__media TwoColumnBanner__media--contain" style="background-color: rgba(255, 255, 255, 1);"> <img class="TwoColumnBanner__image" src="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2021.png?width=1893&height=1537&name=Spot%20Image%2021.png" alt="Spot Image 21" width="1893" height="1537" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2021.png?width=947&height=769&name=Spot%20Image%2021.png 947w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2021.png?width=1893&height=1537&name=Spot%20Image%2021.png 1893w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2021.png?width=2840&height=2306&name=Spot%20Image%2021.png 2840w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2021.png?width=3786&height=3074&name=Spot%20Image%2021.png 3786w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2021.png?width=4733&height=3843&name=Spot%20Image%2021.png 4733w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2021.png?width=5679&height=4611&name=Spot%20Image%2021.png 5679w" sizes="(max-width: 1893px) 100vw, 1893px"> </div> </div> </div></div> </div> </div> </div> <div class="row-fluid-wrapper row-depth-1 row-number-6 "> <div class="row-fluid "> <div class="span4 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="0" data-w="4"> <div id="hs_cos_wrapper_widget_1662805848347" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="TwoColumnBanner TwoColumnBanner--list TwoColumnBanner--no-grid border TwoColumnBanner--flip "> <div class="grid grid--cols-2"> <div class="TwoColumnBanner__text grid-padding"> <div class="TwoColumnBanner--centre-content"> <p class="supertitle">Features of JKlustor</p> <div class="flow "><h3>Similarity based clustering</h3></div> <div class="IconList"> <div class="IconListItem"> <img class="IconListItem__image" src="https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%204@4x.png?width=199&height=199&name=ABSTRACT%20SCIENTIFIC%204@4x.png" alt="ABSTRACT SCIENTIFIC 4@4x" width="199" height="199" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%204@4x.png?width=100&height=100&name=ABSTRACT%20SCIENTIFIC%204@4x.png 100w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%204@4x.png?width=199&height=199&name=ABSTRACT%20SCIENTIFIC%204@4x.png 199w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%204@4x.png?width=299&height=299&name=ABSTRACT%20SCIENTIFIC%204@4x.png 299w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%204@4x.png?width=398&height=398&name=ABSTRACT%20SCIENTIFIC%204@4x.png 398w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%204@4x.png?width=498&height=498&name=ABSTRACT%20SCIENTIFIC%204@4x.png 498w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%204@4x.png?width=597&height=597&name=ABSTRACT%20SCIENTIFIC%204@4x.png 597w" sizes="(max-width: 199px) 100vw, 199px"> <div class="IconListItem__text"> <h4> <strong>Hierarchical method:</strong><span> </span> </h4> <p><span>Ward’s minimum variance method, speeded up with Murtagh’s reciprocal nearest neighbour algorithm, creates tight and well separated clusters. It's recommended to use it with smaller data sets, like focused libraries with less than 100,000 structures. </span><a href="https://docs.chemaxon.com/display/docs/ward-clustering.md">More on Ward clustering</a></p> </div> </div> <div class="IconListItem"> <img class="IconListItem__image" src="https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%201@4x.png?width=198&height=199&name=ABSTRACT%20SCIENTIFIC%201@4x.png" alt="ABSTRACT SCIENTIFIC 1@4x" width="198" height="199" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%201@4x.png?width=99&height=100&name=ABSTRACT%20SCIENTIFIC%201@4x.png 99w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%201@4x.png?width=198&height=199&name=ABSTRACT%20SCIENTIFIC%201@4x.png 198w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%201@4x.png?width=297&height=299&name=ABSTRACT%20SCIENTIFIC%201@4x.png 297w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%201@4x.png?width=396&height=398&name=ABSTRACT%20SCIENTIFIC%201@4x.png 396w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%201@4x.png?width=495&height=498&name=ABSTRACT%20SCIENTIFIC%201@4x.png 495w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/ABSTRACT%20SCIENTIFIC%201@4x.png?width=594&height=597&name=ABSTRACT%20SCIENTIFIC%201@4x.png 594w" sizes="(max-width: 198px) 100vw, 198px"> <div class="IconListItem__text"> <h4>Non-hierarchical method:</h4> <p><span>The </span><a href="https://docs.chemaxon.com/display/docs/Sphere+Exclusion+clustering">Sphere Exclusion clustering</a><span> is based on fingerprints and/or other numerical data, it can easily cope with millions of structures and it is suitable for diverse subset selection. </span><a href="https://docs.chemaxon.com/display/docs/K-means+clustering">K-means cluster analysis</a><span> method aims to find the center of natural clusters in the input data in a way that minimizes the variance within each cluster. Finally, the </span><a href="https://docs.chemaxon.com/display/docs/Jarvis-Patrick+clustering">Jarvis-Patrick (Jarp) method</a><span> uses a nearest neighbor approach and performs variable-length clustering of chemical databases with hundreds of thousands of structures contained.</span></p> </div> </div> </div> </div> </div> <div class="TwoColumnBanner__media TwoColumnBanner__media--cover"> <img class="TwoColumnBanner__image" src="https://chemaxon.com/hs-fs/hubfs/sphere_exclusion_clustering_with_jklustor.jpg?width=345&height=334&name=sphere_exclusion_clustering_with_jklustor.jpg" alt="sphere_exclusion_clustering_with_jklustor" width="345" height="334" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/sphere_exclusion_clustering_with_jklustor.jpg?width=173&height=167&name=sphere_exclusion_clustering_with_jklustor.jpg 173w, https://chemaxon.com/hs-fs/hubfs/sphere_exclusion_clustering_with_jklustor.jpg?width=345&height=334&name=sphere_exclusion_clustering_with_jklustor.jpg 345w, https://chemaxon.com/hs-fs/hubfs/sphere_exclusion_clustering_with_jklustor.jpg?width=518&height=501&name=sphere_exclusion_clustering_with_jklustor.jpg 518w, https://chemaxon.com/hs-fs/hubfs/sphere_exclusion_clustering_with_jklustor.jpg?width=690&height=668&name=sphere_exclusion_clustering_with_jklustor.jpg 690w, https://chemaxon.com/hs-fs/hubfs/sphere_exclusion_clustering_with_jklustor.jpg?width=863&height=835&name=sphere_exclusion_clustering_with_jklustor.jpg 863w, https://chemaxon.com/hs-fs/hubfs/sphere_exclusion_clustering_with_jklustor.jpg?width=1035&height=1002&name=sphere_exclusion_clustering_with_jklustor.jpg 1035w" sizes="(max-width: 345px) 100vw, 345px"> </div> </div> </div></div> </div> <div class="span4 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="4" data-w="4"> <div id="hs_cos_wrapper_module_1662806036160" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="TwoColumnBanner TwoColumnBanner--list TwoColumnBanner--no-grid border "> <div class="grid grid--cols-2"> <div class="TwoColumnBanner__text grid-padding"> <div class="TwoColumnBanner--centre-content"> <p class="supertitle">Features of JKlustor</p> <div class="flow "><h3>Structure based clustering</h3></div> <div class="IconList"> <div class="IconListItem"> <img class="IconListItem__image" src="https://chemaxon.com/hs-fs/hubfs/Pictrograms/SELECT@4x.png?width=199&height=199&name=SELECT@4x.png" alt="SELECT@4x" width="199" height="199" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/Pictrograms/SELECT@4x.png?width=100&height=100&name=SELECT@4x.png 100w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/SELECT@4x.png?width=199&height=199&name=SELECT@4x.png 199w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/SELECT@4x.png?width=299&height=299&name=SELECT@4x.png 299w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/SELECT@4x.png?width=398&height=398&name=SELECT@4x.png 398w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/SELECT@4x.png?width=498&height=498&name=SELECT@4x.png 498w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/SELECT@4x.png?width=597&height=597&name=SELECT@4x.png 597w" sizes="(max-width: 199px) 100vw, 199px"> <div class="IconListItem__text"> <h4> <strong>Hierarchical methods:</strong><span> </span> </h4> <p><span> </span><a href="https://docs.chemaxon.com/display/docs/library-mcs-libmcs-clustering.md">LibraryMCS</a><span> identifies the largest substructure shared by several molecular structures. It uses the hierarchical representation of clusters (dendograms), and it vizualizes an alternative tree and table view too. </span><a href="https://docs.chemaxon.com/display/docs/maximum-common-substructure-mcs-search.md">MCS profiling</a><span> helps scientists explore screening results to quickly identify novel scaffolds and new examples of active compound families. The hierarchical SAR table enables viewing of clusters and associated non-structural data. R-group decomposition can be also performed using the MCS as the core structure for each cluster.</span></p> </div> </div> <div class="IconListItem"> <img class="IconListItem__image" src="https://chemaxon.com/hs-fs/hubfs/Pictrograms/DESIGN@4x.png?width=199&height=199&name=DESIGN@4x.png" alt="DESIGN@4x" width="199" height="199" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/Pictrograms/DESIGN@4x.png?width=100&height=100&name=DESIGN@4x.png 100w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/DESIGN@4x.png?width=199&height=199&name=DESIGN@4x.png 199w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/DESIGN@4x.png?width=299&height=299&name=DESIGN@4x.png 299w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/DESIGN@4x.png?width=398&height=398&name=DESIGN@4x.png 398w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/DESIGN@4x.png?width=498&height=498&name=DESIGN@4x.png 498w, https://chemaxon.com/hs-fs/hubfs/Pictrograms/DESIGN@4x.png?width=597&height=597&name=DESIGN@4x.png 597w" sizes="(max-width: 199px) 100vw, 199px"> <div class="IconListItem__text"> <h4>Non-hierarchical method:</h4> <p><span>JKlustor makes clustering available for pre-generated use </span><a href="https://docs.chemaxon.com/display/docs/Bemis-Murcko+clustering">Bemis-Murcko frameworks</a><span> structures, and therefore provides a convenient and quick way towards analyzing large databases with millions of compounds.</span></p> </div> </div> </div> </div> </div> <div class="TwoColumnBanner__media TwoColumnBanner__media--contain"> <img class="TwoColumnBanner__image" src="https://chemaxon.com/hs-fs/hubfs/dendogram.png?width=1500&height=771&name=dendogram.png" alt="dendogram" width="1500" height="771" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/dendogram.png?width=750&height=386&name=dendogram.png 750w, https://chemaxon.com/hs-fs/hubfs/dendogram.png?width=1500&height=771&name=dendogram.png 1500w, https://chemaxon.com/hs-fs/hubfs/dendogram.png?width=2250&height=1157&name=dendogram.png 2250w, https://chemaxon.com/hs-fs/hubfs/dendogram.png?width=3000&height=1542&name=dendogram.png 3000w, https://chemaxon.com/hs-fs/hubfs/dendogram.png?width=3750&height=1928&name=dendogram.png 3750w, https://chemaxon.com/hs-fs/hubfs/dendogram.png?width=4500&height=2313&name=dendogram.png 4500w" sizes="(max-width: 1500px) 100vw, 1500px"> </div> </div> </div></div> </div> <div class="span4 widget-span widget-type-cell dnd-column" style="" data-widget-type="cell" data-x="8" data-w="4"> <div class="row-fluid-wrapper row-depth-2 row-number-1 "> <div class="row-fluid "> <div class="span6 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="0" data-w="6"> <div id="hs_cos_wrapper_module_1662803063423" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="TwoColumnBanner "> <div class="grid grid--cols-2 grid--align-end"> <div class="TwoColumnBanner__text grid-padding"> <p class="supertitle">Features of JKlustor</p> <div class="flow xl-heading"><h3>Extending capabilities with descriptors and command line tools</h3> <p>JKlustor can use Chemaxon’s proprietary<span> </span><a href="https://docs.chemaxon.com/display/docs/Chemical+Fingerprints">chemical and pharmacophore fingerprint</a><span> </span>technology, and also other user defined descriptors such as BCUT. For example, predicted or measured<span> </span><a href="/calculators-and-predictors?hsLang=en">phys-chem properties</a><span> </span>(like pKa, logP etc.) can also help with clustering.</p> <p>Command line tools in JKlustor:</p> <ul> <li>Diversity analysis - with Compr command line it generates different types of similarity or dissimilarity comparisons within a dataset (also see<span> </span><a href="https://docs.chemaxon.com/display/docs/diverse-set-selection.md">Diversity Set Selection</a>) .</li> <li> <a href="https://docs.chemaxon.com/display/docs/fingerprint-and-descriptor-generation-generatemd.md">GenerateMD</a><span> </span>- generates molecular descriptors for molecular stuctures.</li> <li> <a href="https://docs.chemaxon.com/display/docs/Jarvis-Patrick+clustering">Jarp</a><span> </span>- clustering by a modified Jarvis-Patrick method.</li> <li> <a href="https://docs.chemaxon.com/display/docs/Ward+clustering">Ward</a><span> </span>- clustering by Ward's hierarchic clustering method using the RNN approach.</li> <li> <a href="https://docs.chemaxon.com/display/docs/MCS+search+and+LibMCS">LibMCS</a><span> </span>- Maximum Common Substructure based hierarchical clustering.</li> <li> <a href="https://docs.chemaxon.com/display/docs/CreateView">CreateView</a><span> </span>- composing a new SDfile from an SDfile and a data table - It's useful for viewing the clustered results.</li> </ul></div> </div> <div class=" TwoColumnBanner__media TwoColumnBanner__media--contain" style="background-color: rgba(255, 255, 255, 1);"> <img class="TwoColumnBanner__image" src="https://chemaxon.com/hs-fs/hubfs/product-1.png?width=1893&height=1537&name=product-1.png" alt="product-1" width="1893" height="1537" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/product-1.png?width=947&height=769&name=product-1.png 947w, https://chemaxon.com/hs-fs/hubfs/product-1.png?width=1893&height=1537&name=product-1.png 1893w, https://chemaxon.com/hs-fs/hubfs/product-1.png?width=2840&height=2306&name=product-1.png 2840w, https://chemaxon.com/hs-fs/hubfs/product-1.png?width=3786&height=3074&name=product-1.png 3786w, https://chemaxon.com/hs-fs/hubfs/product-1.png?width=4733&height=3843&name=product-1.png 4733w, https://chemaxon.com/hs-fs/hubfs/product-1.png?width=5679&height=4611&name=product-1.png 5679w" sizes="(max-width: 1893px) 100vw, 1893px"> </div> </div> </div></div> </div> <div class="span6 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="6" data-w="6"> <div id="hs_cos_wrapper_module_1662806823634" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="TwoColumnBanner TwoColumnBanner--flip"> <div class="grid grid--cols-2 grid--align-end"> <div class="TwoColumnBanner__text grid-padding"> <p class="supertitle">JKlustor Benefits</p> <div class="flow xl-heading"><h3>Availability</h3> <p>JKlustor tools can be called upon from the command line or from the API of JChem. JKlustor runs on many operating systems and can integrate with many database engines. Full Java and .NET integration is supported, as well as, connected to Oracle, MySQL, MS SQL Server, DB2, PostgreSQL, Access, etc. databases. The LibMCS element comes with a standalone GUI that allows users to browse/navigate through large sets of data. Furthermore, maximum common edge sub-graph (MCES) and maximum common substructure (MCS) clustering methods are also available as Chemaxon components, for both, KNIME and Pipeline Pilot workflow management systems.</p></div> </div> <div class=" TwoColumnBanner__media TwoColumnBanner__media--contain" style="background-color: rgba(255, 255, 255, 1);"> <img class="TwoColumnBanner__image" src="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2023.png?width=1893&height=1537&name=Spot%20Image%2023.png" alt="Spot Image 23" width="1893" height="1537" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2023.png?width=947&height=769&name=Spot%20Image%2023.png 947w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2023.png?width=1893&height=1537&name=Spot%20Image%2023.png 1893w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2023.png?width=2840&height=2306&name=Spot%20Image%2023.png 2840w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2023.png?width=3786&height=3074&name=Spot%20Image%2023.png 3786w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2023.png?width=4733&height=3843&name=Spot%20Image%2023.png 4733w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Spot%20Image%2023.png?width=5679&height=4611&name=Spot%20Image%2023.png 5679w" sizes="(max-width: 1893px) 100vw, 1893px"> </div> </div> </div></div> </div> </div> </div> </div> </div> </div> <div class="row-fluid-wrapper row-depth-1 row-number-1 "> <div class="row-fluid "> <div class="span12 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="0" data-w="12"> <div id="hs_cos_wrapper_widget_1663316382182" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="SectionTitle border "> <div class="SectionTitle--left grid grid-padding "> <div class="SectionTitle__content" style="max-width:680px"> <div class="flow xl-heading"><h2>Screen Suite</h2> <p> </p></div> </div> </div> </div></div> </div> </div> </div> <div class="row-fluid-wrapper row-depth-1 row-number-2 "> <div class="row-fluid "> <div class="span12 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="0" data-w="12"> <div id="hs_cos_wrapper_widget_1662803041570" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="TwoColumnBanner TwoColumnBanner--flip"> <div class="grid grid--cols-2 grid--align-end"> <div class="TwoColumnBanner__text grid-padding"> <p class="supertitle">Screen Suite Summary</p> <div class="flow xl-heading"><h2>Screen Suite - Toolkit for 2D and 3D molecular screening</h2> <p>The Screen Suite is a ligand-based high throughput virtual screening package that provides powerful tools for chemical (2D) and shape (3D) similarity searches of large molecular libraries. The suite provides several different sets of fingerprints, such as the Chemaxon chemical fingerprint, pharmacophore fingerprint, ECFP/FCFP, dissimilarity metrics and their optimization to tune your processes for optimal search results. Commercially the suite is available as 2D Descriptor package, Screen2D (including our chemical fingerprint) and Screen3D. It is also available as a command line tool, from Java and .NET API and workflow tools like KNIME or Pipeline Pilot. Screen Suite is a progenitor of the novel MadFast similarity search engine, where descriptor generation and similarity search using multiple metrics are also available.</p></div> </div> <div class="expandable TwoColumnBanner__media TwoColumnBanner__media--cover" style="background-color: rgba(255, 255, 255, 1);"> <img class="TwoColumnBanner__image" src="https://chemaxon.com/hubfs/raw_assets/public/Chemaxon/images/placeholders/chemaxon-placeholder-2.jpg" alt="" loading="lazy"> </div> </div> </div></div> </div> </div> </div> </div> <div class="span2 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="2" data-w="2"> <div id="hs_cos_wrapper_module_1662803061866" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="TwoColumnBanner "> <div class="grid grid--cols-2 grid--align-end"> <div class="TwoColumnBanner__text grid-padding"> <p class="supertitle">Screen Suite Features</p> <div class="flow xl-heading"><h3>Flexible descriptor accessibility in Screen Suite</h3> <p>The Screen2D Descriptor package contains<span> </span><a href="https://docs.chemaxon.com/display/docs/Chemical+Fingerprints">fingerprint generators</a><span> </span>for chemical structures, pharmacophores, extended connectivity (ECFP) and functional class (FCFP) descriptors. It can be used to generate and tune fingerprints for use in any screening process. Descriptor generation is supported through Chemaxon’s<span> </span><a href="https://docs.chemaxon.com/display/docs/chemical-terms-introduction.md">Chemical Terms</a><span> </span>scripting language, to create complex fingerprints which consider single or combined molecular attributes that can be based on topological or physicochemical properties like partition coefficients, hydrogen bonding donor-acceptor accessibility or acidic properties.</p></div> </div> <div class="expandable TwoColumnBanner__media TwoColumnBanner__media--contain" style="background-color: rgba(255, 255, 255, 1);"> <img class="TwoColumnBanner__image" src="https://chemaxon.com/hs-fs/hubfs/ecfp_iterations.png?width=224&height=224&name=ecfp_iterations.png" alt="ecfp_iterations" width="224" height="224" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/ecfp_iterations.png?width=112&height=112&name=ecfp_iterations.png 112w, https://chemaxon.com/hs-fs/hubfs/ecfp_iterations.png?width=224&height=224&name=ecfp_iterations.png 224w, https://chemaxon.com/hs-fs/hubfs/ecfp_iterations.png?width=336&height=336&name=ecfp_iterations.png 336w, https://chemaxon.com/hs-fs/hubfs/ecfp_iterations.png?width=448&height=448&name=ecfp_iterations.png 448w, https://chemaxon.com/hs-fs/hubfs/ecfp_iterations.png?width=560&height=560&name=ecfp_iterations.png 560w, https://chemaxon.com/hs-fs/hubfs/ecfp_iterations.png?width=672&height=672&name=ecfp_iterations.png 672w" sizes="(max-width: 224px) 100vw, 224px"> </div> </div> </div></div> </div> <div class="span2 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="4" data-w="2"> <div id="hs_cos_wrapper_module_1662807089120" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="TwoColumnBanner TwoColumnBanner--flip"> <div class="grid grid--cols-2 grid--align-end"> <div class="TwoColumnBanner__text grid-padding"> <p class="supertitle">Screen Suite Features</p> <div class="flow xl-heading"><h3>Diverse fingerprints</h3> <p>Chemaxon's screening technology heavily relies on the available chemical fingerprints and molecular descriptors:</p> <ul> <li> <a href="https://docs.chemaxon.com/display/docs/fingerprint-and-descriptor-generation-generatemd.md#Fingerprintanddescriptorgeneration-GenerateMD-BCUTdescriptors">BCUT descriptors</a><span> </span>- used in diversity analyses and QSAR; based on the connectivity table of molecules with physchem properties like atomic charge, HBDA and polarizability</li> <li> <a href="https://docs.chemaxon.com/display/docs/chemical-hashed-fingerprint.md">Chemical fingerprint</a><span> </span>- used for structural searches in databases, similarity search or diversity analysis of compound libraries; it is a path-based bit-string descriptor describing molecular structures</li> <li> <a href="https://docs.chemaxon.com/display/docs/Pharmacophore+Fingerprint+PF">Pharmacophore fingerprints</a><span> </span>- atom-based fingerprints characterizing binding related structural or physchem properties that are thought to be responsible for pharmacophore activity</li> <li> <a href="https://docs.chemaxon.com/display/docs/extended-connectivity-fingerprint-ecfp.md">Circular fingerprints</a><span> </span>- in contrast to path-based fingerprints ECFP/FCFP are not substructure preserving descriptions, but are highly relevant for full structure and similarity searches.</li> </ul></div> </div> <div class="expandable TwoColumnBanner__media TwoColumnBanner__media--contain" style="background-color: rgba(255, 255, 255, 1);"> <img class="TwoColumnBanner__image" src="https://chemaxon.com/hs-fs/hubfs/cfp_generation.png?width=627&height=351&name=cfp_generation.png" alt="cfp_generation" width="627" height="351" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/cfp_generation.png?width=314&height=176&name=cfp_generation.png 314w, https://chemaxon.com/hs-fs/hubfs/cfp_generation.png?width=627&height=351&name=cfp_generation.png 627w, https://chemaxon.com/hs-fs/hubfs/cfp_generation.png?width=941&height=527&name=cfp_generation.png 941w, https://chemaxon.com/hs-fs/hubfs/cfp_generation.png?width=1254&height=702&name=cfp_generation.png 1254w, https://chemaxon.com/hs-fs/hubfs/cfp_generation.png?width=1568&height=878&name=cfp_generation.png 1568w, https://chemaxon.com/hs-fs/hubfs/cfp_generation.png?width=1881&height=1053&name=cfp_generation.png 1881w" sizes="(max-width: 627px) 100vw, 627px"> </div> </div> </div></div> </div> <div class="span3 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="6" data-w="3"> <div id="hs_cos_wrapper_module_1662807274605" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="TwoColumnBanner "> <div class="grid grid--cols-2 grid--align-end"> <div class="TwoColumnBanner__text grid-padding"> <p class="supertitle">Screen Suite Features</p> <div class="flow xl-heading"><h3>Screen 2D</h3> <p>Screen 2D is a robust platform to perform chemical similarity searches on large molecular databases. It offers a fast process with up to 100,000 compounds per second being screened on a single desktop PC. Modularity of the tool allows to use own descriptor sets. Screen 2D comes with a set of metrics to measure dissimilarity between compounds:</p> <ul> <li>Euclidean</li> <li>Tanimoto</li> <li>Tversky</li> <li>Dice</li> </ul> <p>Screen 2D supports metrics optimization by selecting appropriate training sets. The optimization step increases enrichment significantly, giving smaller, more focused hit sets. It is available through<span> </span><a href="https://docs.chemaxon.com/display/docs/Screen+Developer+Guide">API</a><span> </span>and<span> </span><a href="https://docs.chemaxon.com/display/docs/screenmd.md">command line</a>, via<span> </span>Pipeline Pilot<span> </span>and<span> </span>KNIME<span> </span>connectors, and some features are implemented within<span> </span><a href="/instant-jchem?hsLang=en">Instant JChem</a><span> </span>and<span> </span><a href="/jchem-for-office?hsLang=en">JChem for Office</a><span> </span>desktop applications.</p></div> </div> <div class="expandable TwoColumnBanner__media TwoColumnBanner__media--contain" style="background-color: rgba(255, 255, 255, 1);"> <img class="TwoColumnBanner__image" src="https://chemaxon.com/hs-fs/hubfs/hi-speed.png?width=484&height=336&name=hi-speed.png" alt="hi-speed" width="484" height="336" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/hi-speed.png?width=242&height=168&name=hi-speed.png 242w, https://chemaxon.com/hs-fs/hubfs/hi-speed.png?width=484&height=336&name=hi-speed.png 484w, https://chemaxon.com/hs-fs/hubfs/hi-speed.png?width=726&height=504&name=hi-speed.png 726w, https://chemaxon.com/hs-fs/hubfs/hi-speed.png?width=968&height=672&name=hi-speed.png 968w, https://chemaxon.com/hs-fs/hubfs/hi-speed.png?width=1210&height=840&name=hi-speed.png 1210w, https://chemaxon.com/hs-fs/hubfs/hi-speed.png?width=1452&height=1008&name=hi-speed.png 1452w" sizes="(max-width: 484px) 100vw, 484px"> </div> </div> </div></div> </div> <div class="span3 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="9" data-w="3"> <div id="hs_cos_wrapper_module_1662807273605" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="TwoColumnBanner TwoColumnBanner--flip"> <div class="grid grid--cols-2 grid--align-end"> <div class="TwoColumnBanner__text grid-padding"> <p class="supertitle">Screen Suite Features</p> <div class="flow xl-heading"><div> <h3>Screen 3D</h3> <p>Screen Suite includes 3D shape similarity based searching in addition to topology based screening. It introduces a novel flexible alignment technique, which provides reasonable alternative hit results as compared to previous 3D screen engines. The key feature of Screen 3D is definitely its high speed, however, it also compares very well in providing better enrichment in the first 1% of the hits than most alternative software. Scalability of the tool makes it suitable to search in very large molecular databases.</p> <p>Screen 3D can be used to carry out different shape similarity searches. Beyond fully flexible matching it can align flexible database compounds to rigid query molecules (rigid-flexible). Alternatively it is capable of aligning rigid database compounds to rigid query molecules (rigid-rigid) using on-the-fly generated conformation ensembles. Benefits of Screen3D can also be exploited as a plugin in<a href="/design-hub?hsLang=en" rel="noopener"><span> Design Hub </span></a>idea assessment and management platform.</p> <p><a href="https://docs.chemaxon.com/display/docs/Screen3D">Read more about Screen3D</a></p> </div></div> </div> <div class="expandable TwoColumnBanner__media TwoColumnBanner__media--contain" style="background-color: rgba(255, 255, 255, 1);"> <img class="TwoColumnBanner__image" src="https://chemaxon.com/hs-fs/hubfs/image2.png?width=759&height=714&name=image2.png" alt="3d" width="759" height="714" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/image2.png?width=380&height=357&name=image2.png 380w, https://chemaxon.com/hs-fs/hubfs/image2.png?width=759&height=714&name=image2.png 759w, https://chemaxon.com/hs-fs/hubfs/image2.png?width=1139&height=1071&name=image2.png 1139w, https://chemaxon.com/hs-fs/hubfs/image2.png?width=1518&height=1428&name=image2.png 1518w, https://chemaxon.com/hs-fs/hubfs/image2.png?width=1898&height=1785&name=image2.png 1898w, https://chemaxon.com/hs-fs/hubfs/image2.png?width=2277&height=2142&name=image2.png 2277w" sizes="(max-width: 759px) 100vw, 759px"> </div> </div> </div></div> </div> </div> </div> <div class="row-fluid-wrapper row-depth-1 row-number-3 "> <div class="row-fluid "> <div class="span12 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="0" data-w="12"> <div id="hs_cos_wrapper_module_1662803947748" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="SectionTitle border "> <div class="SectionTitle--left grid grid-padding "> <div class="SectionTitle__content" style="max-width:680px"> <p class="supertitle">Knowledge Hub</p> <div class="flow xl-heading"><h2>Resources</h2> <p>Learn more about Discovery Tools</p></div> </div> </div> </div></div> </div> </div> </div> <div class="row-fluid-wrapper row-depth-1 row-number-4 "> <div class="row-fluid "> <div class="span12 widget-span widget-type-custom_widget dnd-module" style="" data-widget-type="custom_widget" data-x="0" data-w="12"> <div id="hs_cos_wrapper_widget_1661133878842" class="hs_cos_wrapper hs_cos_wrapper_widget hs_cos_wrapper_type_module" style="" data-hs-cos-general-type="widget" data-hs-cos-type="module"> <div class="ListCards border"> <div class="grid grid--cols-4"> <div class="ListCard"> <div class="ListCard__text"> <div class="flow"> <h3>Documentation</h3> </div> </div> <div class="ListCard__image aspect--16-10"> <img class="image--contain" src="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Documents.png?width=1893&height=1537&name=Documents.png" alt="Documents" width="1893" height="1537" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Documents.png?width=947&height=769&name=Documents.png 947w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Documents.png?width=1893&height=1537&name=Documents.png 1893w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Documents.png?width=2840&height=2306&name=Documents.png 2840w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Documents.png?width=3786&height=3074&name=Documents.png 3786w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Documents.png?width=4733&height=3843&name=Documents.png 4733w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Documents.png?width=5679&height=4611&name=Documents.png 5679w" sizes="(max-width: 1893px) 100vw, 1893px"> </div> <div class="ListCard--bottom"> <div class="ListCardItems"> <div class="ListCardItem"> <a href="https://docs.chemaxon.com/display/docs/jklustor.md" target="_blank" rel="noopener"> <p><strong>JKlustor User's Guide</strong></p> </a> </div> <div class="ListCardItem"> <a href="https://dl.chemaxon.com/jchem/config/pharma-calc.xml" target="_blank" rel="noopener"> <p><strong>Pharmacophore Configuration Guide</strong></p> </a> </div> <div class="ListCardItem"> <a href="https://docs.chemaxon.com/display/docs/introduction-to-virtual-screening.md"> Screen Suite User's Guide </a> </div> <div class="ListCardItem"> <a href="https://docs.chemaxon.com/display/docs/screen-developer-guide.md"> Screen Suite Developer's guide </a> </div> </div> </div> </div> <div class="ListCard"> <div class="ListCard__text"> <div class="flow"> <h3>API Docs</h3> </div> </div> <div class="ListCard__image aspect--16-10"> <img class="image--contain" src="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Licensing.png?width=1893&height=1537&name=Licensing.png" alt="Licensing" width="1893" height="1537" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Licensing.png?width=947&height=769&name=Licensing.png 947w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Licensing.png?width=1893&height=1537&name=Licensing.png 1893w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Licensing.png?width=2840&height=2306&name=Licensing.png 2840w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Licensing.png?width=3786&height=3074&name=Licensing.png 3786w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Licensing.png?width=4733&height=3843&name=Licensing.png 4733w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Licensing.png?width=5679&height=4611&name=Licensing.png 5679w" sizes="(max-width: 1893px) 100vw, 1893px"> </div> <div class="ListCard--bottom"> <div class="ListCardItems"> <div class="ListCardItem"> <a href="https://apidocs.chemaxon.com/jchem/doc/dev/java/api/index.html?chemaxon/clustering/package-summary.html" target="_blank" rel="noopener"> <p><strong>JKlustor Java API</strong></p> </a> </div> <div class="ListCardItem"> <a href="https://apidocs.chemaxon.com/dotNET/6.3/API/online/index.html" target="_blank" rel="noopener"> <p><strong>JKlustor .NET API</strong></p> </a> </div> <div class="ListCardItem"> <a href="https://apidocs.chemaxon.com/jchem/doc/dev/java/api/index.html?chemaxon/descriptors/package-summary.html" target="_blank" rel="noopener"> <p><strong>Java API for Molecular Descriptors</strong></p> </a> </div> <div class="ListCardItem"> <a href="https://apidocs.chemaxon.com/dotNET/6.3/API/online/index.html"> Screen Suite .NET API </a> </div> </div> </div> </div> <div class="ListCard"> <div class="ListCard__text"> <div class="flow"> <h3>Training & materials</h3> </div> </div> <div class="ListCard__image aspect--16-10"> <img class="image--contain" src="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Training.png?width=1893&height=1537&name=Training.png" alt="Training" width="1893" height="1537" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Training.png?width=947&height=769&name=Training.png 947w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Training.png?width=1893&height=1537&name=Training.png 1893w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Training.png?width=2840&height=2306&name=Training.png 2840w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Training.png?width=3786&height=3074&name=Training.png 3786w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Training.png?width=4733&height=3843&name=Training.png 4733w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Training.png?width=5679&height=4611&name=Training.png 5679w" sizes="(max-width: 1893px) 100vw, 1893px"> </div> <div class="ListCard--bottom"> <div class="ListCardItems"> <div class="ListCardItem"> <a href="https://chemaxon.com/search?q=JKlustor&hsLang=en" target="_blank" rel="noopener"> <p><strong>JKlustor Library items</strong></p> </a> </div> <div class="ListCardItem"> <a href="https://chemaxon.com/search?q=Screen&hsLang=en" target="_blank" rel="noopener"> <p><strong>Screen Suite Library Items</strong></p> </a> </div> </div> </div> </div> <div class="ListCard"> <div class="ListCard__text"> <div class="flow"> <h3>Support & FAQ</h3> </div> </div> <div class="ListCard__image aspect--16-10"> <img class="image--contain" src="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Help%20and%20support.png?width=1893&height=1537&name=Help%20and%20support.png" alt="Help and support" width="1893" height="1537" loading="lazy" srcset="https://chemaxon.com/hs-fs/hubfs/Spot%20images/Help%20and%20support.png?width=947&height=769&name=Help%20and%20support.png 947w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Help%20and%20support.png?width=1893&height=1537&name=Help%20and%20support.png 1893w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Help%20and%20support.png?width=2840&height=2306&name=Help%20and%20support.png 2840w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Help%20and%20support.png?width=3786&height=3074&name=Help%20and%20support.png 3786w, https://chemaxon.com/hs-fs/hubfs/Spot%20images/Help%20and%20support.png?width=4733&height=3843&name=Help%20and%20support.png 4733w, 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