Ibex: Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins

Dreyer, Frédéric; Ludwiczak, Jan; Martinkus, Karolis; Abanades, Brennan; Alberstein, Robert; Kessel, Pan; Rao, Pranav; Lee, Jae Hyeon; Bonneau, Richard; Watkins, Andrew; Seeger, Franziska

doi:10.5281/zenodo.15866556

Published July 11, 2025 | Version v1

Model Open

Ibex: Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins

1. Genentech
2. Roche (Switzerland)

Model weights of Ibex, an antibody and TCR structure prediction model, available under a Genentech Apache 2.0 Non-Commercial license for non-commercial academic research purposes.

For convenience, the ABodyBuilder3 model weights are also provided, available under a Creative Commons Attribution 4.0 International license for both commercial and non-commercial use.

Both models can be run using the Ibex python package, which is available under an Apache 2.0 license.

Files

Files (555.7 MB)

Name	Size	Download all
abb3.ckpt md5:5a1b9022e0952bb51cc57cbdb6ff1f3d	87.0 MB	Download
ibex_v1.ckpt md5:0bdfea1f533a30d0cd54b9ab7cba42f4	468.7 MB	Download

Additional details

Repository URL: https://github.com/prescient-design/ibex/
Programming language: Python

758

Views

187

Downloads

Show more details

	All versions	This version
Views	758	758
Downloads	187	187
Data volume	63.4 GB	63.4 GB

More info on how stats are collected....

DOI

Resource type

Model

Publisher

Zenodo

License: Genentech Apache 2.0 Non-Commercial

ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF IBEX By downloading, installing, or using the Licensed Software you consent to be bound by and become a party to this agreement (hereinafter "Agreement") as a "LICENSEE". If you do not agree to all of the terms of this Agreement, you must not download, install, or use the Licensed Software, and you do not become a LICENSEE under this Agreement. If you are not a member of an academic research institution, you must obtain a commercial license; please send requests via email to dreyer.frederic@gene.com. This Agreement is entered into by and between Genentech, Inc. (hereinafter "GENENTECH") and the LICENSEE. WHEREAS GENENTECH has the right to license all copyrights and other property rights in the Licensed Software identified as Ibex and developed by GENENTECH and GENENTECH desires to license the Licensed Software so that it becomes available for internal teaching and non-commercial academic research purposes only. WHEREAS LICENSEE is a publicly funded academic and/or education and/or research institution. WHEREAS LICENSEE desires to acquire a free non-exclusive license to use the Licensed Software for internal teaching and non-commercial academic research purposes only. NOW, THEREFORE, in consideration of the mutual promises and covenants contained herein, the parties agree as follows: 1. Definitions "Licensed Software" means the specific version of Ibex pursuant to this Agreement. 2. License Subject to the terms and conditions of this Agreement a non-exclusive, non-transferable license to use and copy the Licensed Software is made available free of charge for the LICENSEE which is a non-profit educational, academic and/or research institution. The license is only granted for internal teaching and non-commercial academic research purposes at one Site, where a Site is defined as a set of contiguous buildings in one location. The Licensed Software will be used at only one location of LICENSEE. This license does not entitle Licensee to receive from GENENTECH copies of the Licensed Software on disks, tapes or CD's, hard-copy documentation, technical support, telephone assistance, or enhancements or updates to the Licensed Software. The user and any research assistants or co-workers who may use the Licensed Software agree to not give the program to third parties or grant licenses on software, which include the Licensed Software, alone or integrated into other software, to third parties. Modification of the source code is prohibited without the prior written consent of GENENTECH. 3. Ownership Except as expressly licensed in this Agreement, GENENTECH shall retain title to the Licensed Software, and any upgrades and modifications created by GENENTECH. 4. Consideration In consideration for the license rights granted by GENENTECH, LICENSEE will obtain this license free of charge. 5. Copies LICENSEE shall have the right to make copies of the Licensed Software for personal and internal teaching and non-commercial academic research purposes at the Site and for back-up purposes under this Agreement, but agrees that all such copies shall contain a copy of this Agreement, copyright notices, and all other reasonable and appropriate proprietary markings or confidential legends that appear on the Licensed Software. 6. Support GENENTECH shall have no obligation to offer support services to LICENSEE, and nothing contained herein shall be interpreted as to require GENENTECH to provide maintenance, installation services, version updates, debugging, consultation or end-user support of any kind. 7. Software Protection LICENSEE acknowledges that the Licensed Software is proprietary to GENENTECH. Except as otherwise expressly permitted in this Agreement, Licensee may not (i) modify or create any derivative works of the Licensed Software or documentation, including customization, translation or localization; (ii) decompile, disassemble, reverse engineer, or otherwise attempt to derive the source code or model weights of the Licensed Software; (iii) redistribute, encumber, sell, rent, lease, sublicense, or otherwise transfer rights to the Licensed Software; (iv) remove or alter any trademark, logo, copyright or other proprietary notices, legends, symbols or labels in the Licensed Software; or (v) publish any results of benchmark tests run on the Licensed Software to a third party without GENENTECH's prior written consent. 8. Representations of GENENTECH to LICENSEE GENENTECH represents to LICENSEE that GENENTECH has the right to grant the License and to enter into this Agreement. 9. Indemnity and Disclaimer of Warranties GENENTECH makes no representations or warranties, express or implied, of any kind. The Licensed Software is provided free of charge, and, therefore, on an "as is" basis, without warranty of any kind, express or implied, including without limitation the warranties that it is free of defects, virus free, able to operate on an uninterrupted basis, merchantable, fit for a particular purpose or non-interfering. The entire risk as to the quality and performance of the Licensed Software is borne by LICENSEE. By way of example, but not limitation, GENENTECH makes no representations or warranties of merchantability or fitness for any particular application or that the use of the Licensed Software will not infringe any patents, copyrights or trademarks or other rights of third parties. The entire risk as to the quality and performance of the Licensed Software is borne by LICENSEE. GENENTECH shall not be liable for any liability or damages with respect to any claim by LICENSEE or any third party on account of, or arising from the license or use of the Licensed Software. Should the Licensed Software prove defective in any respect, LICENSEE and neither GENENTECH should assume the entire cost of any service and repair. This disclaimer of warranty constitutes an essential part of this Agreement. No use of the Licensed Software is authorized hereunder except under this disclaimer. In no event will GENENTECH be liable for any indirect, special, incidental or consequential damages arising out of the use of or inability to use the Licensed Software, including, without limitation, damages for lost profits, loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses, even if advised of the possibility thereof, and regardless of the legal or equitable theory (contract, tort or otherwise) upon which the claim is based. 10. Promotional Advertising & References LICENSEE may not use the name of the Licensed Software in its promotional advertising, product literature, and other similar promotional materials to be disseminated to the public or any portion thereof. LICENSEE agrees not to identify GENENTECH in any promotional advertising or other promotional materials to be disseminated to the public, or any portion thereof without GENENTECH's prior written consent. GENENTECH shall not use LICENSEE's name in publicity or advertising involving this Agreement or otherwise without LICENSEE's prior written consent which may be withheld at LICENSEE's sole discretion. 11. Term This Agreement and the license rights granted herein shall become effective as of the date this Agreement is executed by both parties and shall be perpetual unless terminated in accordance with this Section. GENENTECH may terminate this Agreement at any time. Either party may terminate this Agreement at any time effective upon the other party's breach of any agreement, covenant, or representation made in this Agreement, such breach remaining uncorrected sixty (60) days after written notice thereof. LICENSEE shall have the right, at any time, to terminate this Agreement without cause by written notice to GENENTECH specifying the date of termination. Upon termination, LICENSEE shall destroy all full and partial copies of the Licensed Software. 12. Governing Law This Agreement shall be construed in accordance with the laws of California. 13. General The parties agree that this Agreement is the complete and exclusive agreement among the parties and supersedes all proposals and prior agreements whether written or oral, and all other communications among the parties relating to the subject matter of this Agreement. This Agreement cannot be modified except in writing and signed by both parties. Failure by either party at any time to enforce any of the provisions of this Agreement shall not constitute a waiver by such party of such provision nor in any way affect the validity of this Agreement. The invalidity of singular provisions does not affect the validity of the entire understanding. The parties are obligated, however, to replace the invalid provisions by a regulation which comes closest to the economic intent of the invalid provision. The same shall apply mutatis mutandis in case of a gap. Read more

Technical metadata

Created: July 11, 2025
Modified: January 27, 2026

Ibex: Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins

Authors/Creators

Description

Files

Files (555.7 MB)

Additional details

Software