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eSim3D: ligand-based design - Optibrium
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padding: 0; margin: 0; } html, body { height: 100%; } a { position: absolute; z-index: 9999; inset: 0; } img { position: absolute; inset: 0; width: 100%; height: 100%; object-fit: cover; object-position: center; } span { position: absolute; z-index: 1; inset: 50%; width: 84px; height: 84px; transform: translate(-50%, -50%); } span svg { display: block; width: 100%; }</style><a href="https://www.youtube-nocookie.com/embed/c8KOZw0d_Wo?feature=oembed&autoplay=1&mute=1&modestbranding=1&playsinline=1"><span><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 80 80" fill="none" role="img" aria-hidden="true" width="80" height="80"><path d="M40 75.2c19.441 0 35.2-15.76 35.2-35.2C75.2 20.56 59.442 4.8 40 4.8 20.56 4.8 4.8 20.56 4.8 40c0 19.44 15.76 35.2 35.2 35.2Z" fill="#F9F8F7" fill-opacity=".9"/><path d="M40 75.2c19.441 0 35.2-15.76 35.2-35.2C75.2 20.56 59.442 4.8 40 4.8 20.56 4.8 4.8 20.56 4.8 40c0 19.44 15.76 35.2 35.2 35.2Z" stroke="#000" stroke-width="3.2" stroke-miterlimit="10" stroke-linecap="round" stroke-linejoin="round"/><path d="m30.4 56 27.2-16-27.2-16v32Z" stroke="#000" stroke-width="3.2" stroke-miterlimit="10"/></svg></span><img loading="lazy" src="https://optibrium.com/wp-content/uploads/2024/05/ESM01-Thumbnail-768x432.jpg"></a>" data-image="https://optibrium.com/wp-content/uploads/2024/05/ESM01-Thumbnail-768x432.jpg" title="Introduction to eSim 3D" width="640" height="360" src="https://www.youtube-nocookie.com/embed/c8KOZw0d_Wo?feature=oembed&autoplay=1&mute=1&modestbranding=1&playsinline=1" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe> </div> </div> </div> </div> <section class="in-page-menu wp-block alignwide"> <div class="in-page-menu__outer"> <div class="in-page-menu__inner"> <h2 class="in-page-menu__heading is-style-typestyle-h4">StarDrop’s eSim3D module</h2> <div class="in-page-menu__content nflm"> <p>eSim3D™ <span class="NormalTextRun SCXW253423069 BCX0">supports your </span><span class="NormalTextRun SCXW253423069 BCX0">3D </span><span class="NormalTextRun SCXW253423069 BCX0">ligand-based design efforts, providing intuitive workflows to:</span></p> <ul> <li data-leveltext="" data-font="Symbol" data-listid="1" data-aria-posinset="1" data-aria-level="1"><span data-contrast="auto">Enable 3D design, even with little or no target structure information</span><span data-ccp-props="{"201341983":0,"335559739":0,"335559740":240}"> </span></li> <li data-leveltext="" data-font="Symbol" data-listid="1" data-aria-posinset="2" data-aria-level="1"><span data-contrast="auto">Find novel active compounds with 3D virtual screening against known actives</span><span data-ccp-props="{"201341983":0,"335559739":0,"335559740":240}"> </span></li> <li data-leveltext="" data-font="Symbol" data-listid="1" data-aria-posinset="3" data-aria-level="1"><span data-contrast="auto">Understand 3D SAR</span><span data-contrast="auto"> </span><span data-contrast="auto">with industry-leading pose prediction</span><span data-ccp-props="{"201341983":0,"335559739":0,"335559740":240}"> </span></li> <li data-leveltext="" data-font="Symbol" data-listid="1" data-aria-posinset="3" data-aria-level="1"><span data-contrast="auto">Generate binding mode hypotheses by alignment of multiple known actives</span><span data-ccp-props="{"201341983":0,"335559739":0,"335559740":240}"> </span></li> <li data-leveltext="" data-font="Symbol" data-listid="1" data-aria-posinset="3" data-aria-level="1"><span data-contrast="auto">Complement <a href="https://optibrium.com/products/stardrop/modules/seesar/">structure-based compound design</a> approaches with a ligand-centred perspective</span></li> </ul> </div> </div> <nav class="in-page-menu__nav nflm"> <h3 class="in-page-menu__nav-heading is-style-typestyle-h6">On this page</h3> <ul> <li class="in-page-menu__item"> <a href="https://optibrium.com/products/stardrop/modules/esim3d/#why-esim">Why eSim3D</a> </li> <li class="in-page-menu__item"> <a href="https://optibrium.com/products/stardrop/modules/esim3d/#resources">eSim3D</a> </li> <li class="in-page-menu__item"> <a href="https://optibrium.com/products/stardrop/modules/esim3d/#contact-form">Try eSim3D</a> </li> </ul> </nav> </div> </section> <section id="why-esim" class="stacker wp-block alignfull"> <div class="stacker__outer"> <div class="stacker__inner"> <div class="stacker__header nflm"> <h2 aria-label="How it works" class="stacker__heading is-style-typestyle-h2 has-tags">How it <span>works</span></h2> </div> <div class="stacker__items"> <div class="stacker__item"> <div class="stacker__item-outer has-blue3-background-color"> <div class="stacker__item-inner"> <h3 class="stacker__item-heading is-style-typestyle-h4 has-tags"> State-of-the-art molecular similarity </h3> <div class="stacker__item-content nflm"> <p>Based on surface-shape, electrostatics and directionally-sensitive hydrogen-bonding, the eSim method enables accurate surface-based comparison of molecules. This scaffold-independent method mimics a protein’s perspective of a ligand, improving the accuracy of pose prediction, virtual screening and multiple ligand alignment compared to other molecular similarity methods.</p> </div> </div> <div class="stacker__item-media"> <div class="img-fit"><img decoding="async" width="768" height="768" src="data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHZpZXdCb3g9IjAgMCAxMDAwIDEwMDAiIHdpZHRoPSIxMDAwIiBoZWlnaHQ9IjEwMDAiIGRhdGEtdT0iaHR0cHMlM0ElMkYlMkZvcHRpYnJpdW0uY29tJTJGd3AtY29udGVudCUyRnVwbG9hZHMlMkYyMDI0JTJGMDUlMkZlc2ltX3NxX2hkXzIuanBnIiBkYXRhLXc9IjEwMDAiIGRhdGEtaD0iMTAwMCI+PC9zdmc+" data-spai="1" class="attachment-medium_large size-medium_large" alt="observer points around a molecule" srcset=" " sizes="auto, (max-width: 768px) 100vw, 768px" /></div> </div> </div> </div> <div class="stacker__item"> <div class="stacker__item-outer has-orange-background-color"> <div class="stacker__item-inner"> <h3 class="stacker__item-heading is-style-typestyle-h4 has-tags"> High-performance 3D virtual screening </h3> <div class="stacker__item-content nflm"> <p>Screen millions of compounds, direct from your desktop, in a matter of minutes. eSim’s virtual screening methods have been proven to achieve high enrichment compared to other market platforms. With 3D conformers pre-generated from our vendor library using ForceGen technology, you can screen large collections of purchasable compounds to quickly identify scaffold hops and novel actives.</p> <p>Visit the <a href="https://optibrium.com/resources/?_tax%5Bproduct%5D%5B%5D=&_tax%5Bsolution%5D%5B%5D=&_tax%5Bresource-content-type%5D%5B%5D=90&_tax%5Btopic%5D%5B%5D=">virtual screening downloads</a> section of our site to access prepared virtual screening collections for use in StarDrop.</p> </div> <div class="stacker__item-cta nflm"> <a href="https://optibrium.com/resources/?_tax%5Bproduct%5D%5B%5D=&_tax%5Bsolution%5D%5B%5D=&_tax%5Bresource-content-type%5D%5B%5D=90&_tax%5Btopic%5D%5B%5D=" class="g-button has-arrow">Virtual screening collections</a> </div> </div> <div class="stacker__item-media"> <div class="img-fit"><img decoding="async" width="267" height="284" src="data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHZpZXdCb3g9IjAgMCAyNjcgMjg0IiB3aWR0aD0iMjY3IiBoZWlnaHQ9IjI4NCIgZGF0YS11PSJodHRwcyUzQSUyRiUyRm9wdGlicml1bS5jb20lMkZ3cC1jb250ZW50JTJGdXBsb2FkcyUyRjIwMjMlMkYwOSUyRlZpcnV0YWwtU2NyZWVuLWluLVN1cmZsZXgtZXNpbS1Nb2xQb3J0LWNvbGxlY3Rpb25zLTEucG5nIiBkYXRhLXc9IjI2NyIgZGF0YS1oPSIyODQiPjwvc3ZnPg==" data-spai="1" class="attachment-medium_large size-medium_large" alt="Virtual Screening Snamine screen" /></div> </div> </div> </div> <div class="stacker__item"> <div class="stacker__item-outer has-green-background-color"> <div class="stacker__item-inner"> <h3 class="stacker__item-heading is-style-typestyle-h4 has-tags"> Accurate pose prediction </h3> <div class="stacker__item-content nflm"> <p>Quickly identify the correct molecular alignments. Embedded with physically-meaningful underlying factors, eSim’s pose prediction capabilities have been shown to significantly outperform alternative methods, as proven in several published peer-reviewed benchmarking and validation studies.</p> </div> </div> <div class="stacker__item-media"> <div class="img-fit"><img decoding="async" width="768" height="563" src="data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHZpZXdCb3g9IjAgMCA4ODggNjUxIiB3aWR0aD0iODg4IiBoZWlnaHQ9IjY1MSIgZGF0YS11PSJodHRwcyUzQSUyRiUyRm9wdGlicml1bS5jb20lMkZ3cC1jb250ZW50JTJGdXBsb2FkcyUyRjIwMjQlMkYwNSUyRmVTaW1fMy5wbmciIGRhdGEtdz0iODg4IiBkYXRhLWg9IjY1MSI+PC9zdmc+" data-spai="1" class="attachment-medium_large size-medium_large" alt="eSim3D ligand-based design" srcset=" " sizes="auto, (max-width: 768px) 100vw, 768px" /></div> </div> </div> </div> <div class="stacker__item"> <div class="stacker__item-outer has-blue4-background-color"> <div class="stacker__item-inner"> <h3 class="stacker__item-heading is-style-typestyle-h4 has-tags"> Multiple ligand alignment </h3> <div class="stacker__item-content nflm"> <p>Align multiple known active ligands to generate binding pose hypotheses. These ensembles can be used as targets for virtual screening and to improve our understanding of 3D structure-activity relationships<span class="TextRun SCXW252557202 BCX8" lang="EN-US" xml:lang="EN-US" data-contrast="auto"><span class="NormalTextRun SCXW252557202 BCX8"> to guide lead selection and optimisation.</span></span></p> </div> </div> <div class="stacker__item-media"> <div class="img-fit"><img decoding="async" width="768" height="768" src="data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHZpZXdCb3g9IjAgMCAxMDAwIDEwMDAiIHdpZHRoPSIxMDAwIiBoZWlnaHQ9IjEwMDAiIGRhdGEtdT0iaHR0cHMlM0ElMkYlMkZvcHRpYnJpdW0uY29tJTJGd3AtY29udGVudCUyRnVwbG9hZHMlMkYyMDI0JTJGMDUlMkZlc2ltX3NxX2hkLmpwZyIgZGF0YS13PSIxMDAwIiBkYXRhLWg9IjEwMDAiPjwvc3ZnPg==" data-spai="1" class="attachment-medium_large size-medium_large" alt="eSim molecular similarity model" srcset=" " sizes="auto, (max-width: 768px) 100vw, 768px" /></div> </div> </div> </div> </div> </div> </div> </section> <section id="resources" class="cards wp-block alignfull"> <div class="cards__outer"> <div class="cards__inner"> <div class="cards__header"> <h2 aria-label="3D ligand-based design resources" class="cards__heading is-style-typestyle-h1 has-tags">3D ligand-based design <span>resources</span></h2> </div> <div class="cards__items"> <article class="g-card is-knowledge-base is-publication has-image has-link"> <div class="g-card__outer"> <div class="g-card__inner"> <h2 class="g-card__heading"><a href="https://optibrium.com/knowledge-base/structure-and-ligand-based-virtual-screening-on-dud-e-performance-dependence-on-approximations-to-the-binding-pocket/">Structure- and ligand-based virtual screening on DUD-E+: performance dependence on approximations to the binding pocket</a> </h2> <div class="g-card__content"> <p>Using the DUD-E+ benchmark, we explore the impact of using a single protein pocket or ligand for virtual screening compared with using ensembles of alternative pockets, ligands, and sets thereof.</p> </div> </div> <div class="g-card__footer"> <div class="g-card__labels"> <div class="g-card__labels__items"> <a href="https://optibrium.com/topic/3d-molecular-design/" class="g-button is-small">3D molecular design</a> </div> </div> <div class="g-card__meta"> 9 April 2020 </div> </div> </div> <div class="g-card__media img-fit"> <img decoding="async" width="768" height="349" src="data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHZpZXdCb3g9IjAgMCA5MjggNDIyIiB3aWR0aD0iOTI4IiBoZWlnaHQ9IjQyMiIgZGF0YS11PSJodHRwcyUzQSUyRiUyRm9wdGlicml1bS5jb20lMkZ3cC1jb250ZW50JTJGdXBsb2FkcyUyRjIwMjQlMkYwNSUyRkRVRC1FLXBhcGVyLmpwZWciIGRhdGEtdz0iOTI4IiBkYXRhLWg9IjQyMiI+PC9zdmc+" data-spai="1" class="attachment-medium_large size-medium_large" alt="" id="2687" srcset=" " sizes="auto, (max-width: 768px) 100vw, 768px" /> </div> </article> <article class="g-card is-webinar on-demand has-image has-link"> <div class="g-card__outer"> <div class="g-card__inner"> <span class="g-card__top-meta"> On-demand </span> <h2 class="g-card__heading"><a href="https://optibrium.com/webinars/challenges-and-approaches-in-3d-ligand-based-drug-design/">Challenges and approaches in 3D ligand-based drug design</a> </h2> <div class="g-card__content"> <p>Ann and Ajay discuss the science behind and applications of the eSim molecular similarity method, a ligand-based drug design approach which considers surface-shape, electrostatics, and directionally sensitive hydrogen-bonding when comparing two molecules. </p> </div> </div> <div class="g-card__footer"> <div class="g-card__labels"> <div class="g-card__labels__items"> <a href="https://optibrium.com/topic/3d-molecular-design/" class="g-button is-small">3D molecular design</a> </div> </div> <div class="g-card__meta"> 5 December 2023 </div> </div> </div> <div class="g-card__media img-fit"> <img decoding="async" width="615" height="361" src="data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHZpZXdCb3g9IjAgMCA2MTUgMzYxIiB3aWR0aD0iNjE1IiBoZWlnaHQ9IjM2MSIgZGF0YS11PSJodHRwcyUzQSUyRiUyRm9wdGlicml1bS5jb20lMkZ3cC1jb250ZW50JTJGdXBsb2FkcyUyRjIwMjMlMkYxMiUyRjNELWRydWctZGVzaWduLXdlYmluYXItT2N0LTIwMjMucG5nIiBkYXRhLXc9IjYxNSIgZGF0YS1oPSIzNjEiPjwvc3ZnPg==" data-spai="1" class="attachment-medium_large size-medium_large" alt="" id="2251" /> </div> </article> <article class="g-card is-resource has-image has-link"> <div class="g-card__outer"> <div class="g-card__inner"> <h2 class="g-card__heading"><a href="https://optibrium.com/resources/molport-screening-collection/">MolPort screening collection</a> </h2> <div class="g-card__content"> <p>StarDrop users who have licensed the Surflex eSim3D module can freely download prepared virtual screening collections for use in StarDrop. MolPort’s commercially available screening…</p> </div> </div> <div class="g-card__footer"> <div class="g-card__labels"> <div class="g-card__labels__items"> <a href="https://optibrium.com/topic/virtual-screening/" class="g-button is-small">Virtual Screening</a> </div> </div> <div class="g-card__meta"> 21 June 2024 </div> </div> </div> <div class="g-card__media img-fit"> <img decoding="async" width="768" height="512" src="data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHZpZXdCb3g9IjAgMCAxMjAwIDgwMCIgd2lkdGg9IjEyMDAiIGhlaWdodD0iODAwIiBkYXRhLXU9Imh0dHBzJTNBJTJGJTJGb3B0aWJyaXVtLmNvbSUyRndwLWNvbnRlbnQlMkZ1cGxvYWRzJTJGMjAyMyUyRjExJTJGQ29sbGVjdGlvbi5qcGciIGRhdGEtdz0iMTIwMCIgZGF0YS1oPSI4MDAiPjwvc3ZnPg==" data-spai="1" class="attachment-medium_large size-medium_large" alt="" id="4626" srcset=" " sizes="auto, (max-width: 768px) 100vw, 768px" /> </div> </article> </div> </div> </div> </section> <section id="contact-form" class="two-column-content wp-block alignwide"> <div class="two-column-content__outer"> <div class="two-column-content__column nflm is-first"> <h2 aria-label="Interested in 3D ligand-based design?" class="two-column-content__heading is-style-typestyle-h1 has-tags">Interested in <span>3D ligand-based design?</span></h2> <div class="two-column-content__content nflm"> <p>Would you like to try the eSim3D module? 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