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Dataset Description:

The Consistency Distilled Synthetic Protein Database is a curated collection of high-quality, codesignable protein sequence–structure pairs designed to overcome limitations present in datasets derived from the AlphaFold Database (AFDB). The existing AFDB contains pairs that are not reproducible by state-of-the-art folding models such as ESMFold, AlphaFold2, or Boltz-1, indicating that many sequences may not accurately fold into their predicted structures. To address this, the Proteina-Atomistica Consistency Distilled Database was built from scratch using ProteinMPNN to generate multiple synthetic sequences for each Foldseek AFDB cluster representative structure. These sequences were then re-folded to obtain fully atomistic, self-consistent models. The result aligns the diversity of the original AFDB with the consistency of inverse folding and re-folding.

This dataset is ready for commercial/non-commercial use.

Dataset Owner(s):

NVIDIA Corporation

Dataset Creation Date:

5/15/2025

License/Terms of Use:

CC_BY-4.0

Intended Usage:

Protein designers and researchers alike who wish to scale their protein AI models to predict structure, sequences, and properties.

Dataset Quantification

Record count: 455,473 protein structures

Feature count: 6 metadata features for each structure (id, length, plddt_avg, plddt_std, rmsd_ca, pmpnn_seq)

Measurement of Total Data Storage: 10.96 GB

Reference(s):

https://arxiv.org/pdf/2512.01976

Ethical Considerations:

NVIDIA believes Trustworthy AI is a shared responsibility and we have established policies and practices to enable development for a wide array of AI applications. When downloaded or used in accordance with our terms of service, developers should work with their internal model team to ensure this model meets requirements for the relevant industry and use case and addresses unforeseen product misuse.
\nPlease report model quality, risk, security vulnerabilities or NVIDIA AI Concerns (https://app.intigriti.com/programs/nvidia/nvidiavdp/detail).

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The existing AFDB contains pairs that are not reproducible by state-of-the-art folding models such as ESMFold, AlphaFold2, or Boltz-1, indicating that many sequences may not accurately fold into their predicted structures. To address this, the Proteina-Atomistica Consistency Distilled Database was built from scratch using ProteinMPNN to generate multiple synthetic sequences for each Foldseek AFDB cluster representative structure. These sequences were then re-folded to obtain fully atomistic, self-consistent models. The result aligns the diversity of the original AFDB with the consistency of inverse folding and re-folding.\n\nThis dataset is ready for commercial/non-commercial use.\n\n## Dataset Owner(s):\nNVIDIA Corporation\n\n## Dataset Creation Date:\n5/15/2025\n\n## License/Terms of Use: \nCC_BY-4.0\n\n## Intended Usage:\nProtein designers and researchers alike who wish to scale their protein AI models to predict structure, sequences, and properties.\n\n## Dataset Quantification\nRecord count: 455,473 protein structures\n\nFeature count: 6 metadata features for each structure (id, length, plddt_avg, plddt_std, rmsd_ca, pmpnn_seq)\n\nMeasurement of Total Data Storage: 10.96 GB\n\n## Reference(s):\nhttps://arxiv.org/pdf/2512.01976 \n\n## Ethical Considerations:\nNVIDIA believes Trustworthy AI is a shared responsibility and we have established policies and practices to enable development for a wide array of AI applications. 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As part of our bot management service, this cookie helps manage incoming traffic that matches criteria associated with bots.\nThis is a CloudFoundry cookie","OptanonConsent","nvid.nvidia.com","This cookie is set by the cookie compliance solution from OneTrust. It stores information about the categories of cookies the site uses and whether visitors have given or withdrawn consent for the use of each category. This enables site owners to prevent cookies in each category from being set in the users browser, when consent is not given. The cookie has a normal lifespan of one year, so that returning visitors to the site will have their preferences remembered. It contains no information that can identify the site visitor.","events.nvidia.com","This cookie is associated with the Amazon Web Services Elastic Load Balancing functionality for routing client request on the server.Used to attribute commission to affiliates when you arrive at the website from an affiliate referral link. It is set when you click on one of our links and used to let the advertiser and us know the website from which you came.","sessionid","This is a very generic cookie name that may have different purposes on different sites, but generally it will be some kind of anonymous session identifier.","_csrf","This cookie is used to prevent Cross-Site Request Forgery (CSRF) attacks, ensuring that each request made to the server is from the user's browser and is intentional.","enterprise-support.nvidia.com","Used to apply end-user cookie consent preferences set by our client-side utility.Custom- Short Duration. Unique ID of an Enquiry- used to validate access to case, and load exisiting data.\n","renderCtx","academicgrants.nvidia.com","Used to store site parameters in the session for reuse across requests by a single client for functionality and performance reasons.","ph_phc_yQgAEdJJkVpI24NdSRID2mor1x1leRpDoC9yZ9mfXal_posthog","The PostHog ph_phc_xxx cookie is a session cookie used for identifying and tracking visitors on websites, helping us understand user behavior and website performance.","This cookie is managed by AWS and is used for load balancing.Used to attribute commission to affiliates when you arrive at the website from an affiliate referral link. It is set when you click on one of our links and used to let the advertiser and us know the website from which you came.","This cookie is associated with Akamai and is used to differentiate between traffic from humans and bots.","OptanonAlertBoxClosed","docs.ngc.nvidia.com","This cookie is set by websites using certain versions of the cookie law compliance solution from OneTrust. It is set after visitors have seen a cookie information notice and in some cases only when they actively close the notice down. It enables the website not to show the message more than once to a user. The cookie has a normal lifespan of one year and contains no personal information.","nv_co","__uxq412__ses.88c1","investor.nvidia.com","learn.learn.nvidia.com","This cookie is associated with the Amazon Web Services Elastic Load Balancing functionality for routing client request on the server.","pctrk","Used to count page views by unauthenticated users against license usage.","bm_s","bpazaws52gukakzc__ctrl0_ctl36_uccaptcha","bm_sv","store.nvidia.com","The __cf_bm cookie is a cookie necessary to support Cloudflare Bot Management, currently in private beta. As part of our bot management service, this cookie helps manage incoming traffic that matches criteria associated with bots.\n","This cookie name is used by DataDog to determine if cookies are supported on the website.dd_cookie_test","AMP_TLDTEST_xxxxxxxx","SESSlsd","This cookie is likely to be a session identifier used to maintain user session state across page requests.","mboxEdgeCluster","This cookie name is associated with Adobe Target which is used to communicate the correct edge cluster to at.js so that Target profiles can stay in sync as users navigate across a site.","_biz_pendingA","_rdt_em","This cookie name is associated with Reddit which is used to manage session state and user interactions.","megaNavCollapsed","_abck","The _abck cookie is associated with Akamai's Bot Manager, which is used to prevent fraud and abuse by safeguarding online interactions and detecting irregularities that could suggest malicious activity, such as bot-driven attacks or hacking attempts.","AMP_TEST","This cookie name AMP_TEST is used for internal analytics by the website operator, necessary for the functionality of the website's chat-box function, and to check whether the cookie storage is working properly.","idccsrf","This cookie name is associated with Salesforce which is used to track CrossSiteRequestForgery validation for certain single sign-on (SSO) flows.","_biz_flagsA","This cookie is used to remember users' settings as well as for authentication and analytics.","ApplicationGatewayAffinity","partners.nvidia.com","This cookie is used to maintain a user session by the server in a load balanced environment, to ensure the user has a consistent experience.","AMP_TEST_xxxxxxxx","bm_lso","This cookie name is associated with Akamai which is used to load the site as quickly as possible and to recognize bots.","SSESS###########","This cookie is likely to be a session cookie used to maintain an anonymized user session by the server in a secure environment, often seen in sites built with the Drupal content management system.","nvdeveloper.nvidia.com","__uxq412__id.88c1","QueueITAccepted-SDFrts345E-V3_{eventId}","TEST_AMCV_COOKIE_WRITE","This cookie is used to test whether cookies are enabled in the browser. 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It is set when you click on one of our links and used to let the advertiser and us know the website from which you came.","_devzone_session","This cookie is likely used to maintain a user session on the website by the server. It is common for session identifiers to be used to keep users logged in and track their interaction with the site during a session.","_cs_c","The cookie is used by Content Square to save the user consent to be tracked.","bm_sz","This cookie is used by Akamai to optimize site performance and security. It is typically associated with the delivery of web content and services.","vcalliance.nvidia.com","ASP.NET_SessionId","General purpose platform session cookie, used by sites written with Microsoft .NET based technologies. 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