guest ::
| Home > Publications database > Improved protein binder design using β-pairing targeted RFdiffusion > print |
| Home > Publications database > Improved protein binder design using β-pairing targeted RFdiffusion > print |
| 001 | 646221 | ||
| 005 | 20260218211012.0 | ||
| 024 | 7 | _ | |a 10.1038/s41467-025-67866-3 |2 doi |
| 024 | 7 | _ | |a 10.3204/PUBDB-2026-00766 |2 datacite_doi |
| 037 | _ | _ | |a PUBDB-2026-00766 |
| 041 | _ | _ | |a English |
| 082 | _ | _ | |a 500 |
| 100 | 1 | _ | |a Sappington, Isaac |0 0000-0002-1073-0643 |b 0 |
| 245 | _ | _ | |a Improved protein binder design using β-pairing targeted RFdiffusion |
| 260 | _ | _ | |a [London] |c 2026 |b Springer Nature |
| 336 | 7 | _ | |a article |2 DRIVER |
| 336 | 7 | _ | |a Output Types/Journal article |2 DataCite |
| 336 | 7 | _ | |a Journal Article |b journal |m journal |0 PUB:(DE-HGF)16 |s 1771420883_1981152 |2 PUB:(DE-HGF) |
| 336 | 7 | _ | |a ARTICLE |2 BibTeX |
| 336 | 7 | _ | |a JOURNAL_ARTICLE |2 ORCID |
| 336 | 7 | _ | |a Journal Article |0 0 |2 EndNote |
| 520 | _ | _ | |a Designing proteins that bind with high affinity to hydrophilic protein target sites remains a challenging problem. Here we show that RFdiffusion can be conditioned to generate protein scaffolds that form geometrically matched extended β-sheets with target protein edge β-strands in which polar groups on the target are complemented with hydrogen bonding groups on the design. We use this approach to design binders against edge-strand target sites on KIT, PDGFRɑ, ALK-2, ALK-3, FCRL5, NRP1, and α-CTX, and obtain higher (pM to mid nM) affinities and success rates than unconditioned RFdiffusion. Despite sharing β-strand interactions, designs have high specificity, reflecting the precise customization of interacting β-strand geometry and additional designed binder-target interactions. A binder-KIT co-crystal structure is nearly identical to the design model, confirming the accuracy of the design approach. The ability to robustly generate binders to the hydrophilic interaction surfaces of exposed β-strands considerably increases the range of computational binder design. |
| 536 | _ | _ | |a 6G3 - PETRA III (DESY) (POF4-6G3) |0 G:(DE-HGF)POF4-6G3 |c POF4-6G3 |f POF IV |x 0 |
| 588 | _ | _ | |a Dataset connected to CrossRef, Journals: bib-pubdb1.desy.de |
| 693 | _ | _ | |a PETRA III |f PETRA Beamline P13 |1 EXP:(DE-H253)PETRAIII-20150101 |0 EXP:(DE-H253)P-P13-20150101 |6 EXP:(DE-H253)P-P13-20150101 |x 0 |
| 700 | 1 | _ | |a Toul, Martin |0 P:(DE-HGF)0 |b 1 |
| 700 | 1 | _ | |a Lee, David S. |0 0000-0001-6539-4272 |b 2 |
| 700 | 1 | _ | |a Robinson, Stephanie A. |b 3 |
| 700 | 1 | _ | |a Goreshnik, Inna |b 4 |
| 700 | 1 | _ | |a McCurdy, Clara |0 0009-0008-8120-9776 |b 5 |
| 700 | 1 | _ | |a Chan, Tung Ching |b 6 |
| 700 | 1 | _ | |a Buchholz, Nic |b 7 |
| 700 | 1 | _ | |a Huang, Buwei |b 8 |
| 700 | 1 | _ | |a Vafeados, Dionne |0 0000-0002-2560-8907 |b 9 |
| 700 | 1 | _ | |a Garcia-Sanchez, Mariana |0 0009-0002-9194-0251 |b 10 |
| 700 | 1 | _ | |a Roullier, Nicole |0 0009-0004-8430-9538 |b 11 |
| 700 | 1 | _ | |a Glögl, Matthias |b 12 |
| 700 | 1 | _ | |a Kim, Christopher J. |0 0000-0003-4305-0473 |b 13 |
| 700 | 1 | _ | |a Watson, Joseph L. |0 0000-0001-5492-0249 |b 14 |
| 700 | 1 | _ | |a Torres, Susana Vázquez |b 15 |
| 700 | 1 | _ | |a Verschueren, Koen H. G. |b 16 |
| 700 | 1 | _ | |a Verstraete, Kenneth |b 17 |
| 700 | 1 | _ | |a Hinck, Cynthia S. |b 18 |
| 700 | 1 | _ | |a Benard-Valle, Melisa |0 0000-0002-0042-6592 |b 19 |
| 700 | 1 | _ | |a Coventry, Brian |0 0000-0002-6910-6255 |b 20 |
| 700 | 1 | _ | |a Sims, Jeremiah Nelson |0 0000-0002-0479-0367 |b 21 |
| 700 | 1 | _ | |a Ahn, Green |0 0000-0003-4482-2754 |b 22 |
| 700 | 1 | _ | |a Wang, Xinru |b 23 |
| 700 | 1 | _ | |a Hinck, Andrew P. |0 0000-0003-3320-8054 |b 24 |
| 700 | 1 | _ | |a Jenkins, Timothy P. |0 0000-0003-2979-5663 |b 25 |
| 700 | 1 | _ | |a Ruohola-Baker, Hannele |0 0000-0002-5588-4531 |b 26 |
| 700 | 1 | _ | |a Banik, Steven M. |0 0000-0002-0544-6488 |b 27 |
| 700 | 1 | _ | |a Savvides, Savvas N. |b 28 |
| 700 | 1 | _ | |a Baker, David |0 P:(DE-H253)PIP1104266 |b 29 |e Corresponding author |
| 773 | _ | _ | |a 10.1038/s41467-025-67866-3 |g Vol. 17, no. 1, p. 1101 |0 PERI:(DE-600)2553671-0 |n 1 |p 1101 |t Nature Communications |v 17 |y 2026 |x 2041-1723 |
| 856 | 4 | _ | |u https://www.nature.com/articles/s41467-025-67866-3#article-info |
| 856 | 4 | _ | |u https://bib-pubdb1.desy.de/record/646221/files/Improved%20protein%20binder%20design%20using%20beta%20pairing%20targeted%20RFdiffusion.pdf |y OpenAccess |
| 856 | 4 | _ | |u https://bib-pubdb1.desy.de/record/646221/files/Improved%20protein%20binder%20design%20using%20beta%20pairing%20targeted%20RFdiffusion.pdf?subformat=pdfa |x pdfa |y OpenAccess |
| 909 | C | O | |o oai:bib-pubdb1.desy.de:646221 |p openaire |p open_access |p VDB |p driver |p dnbdelivery |
| 910 | 1 | _ | |a External Institute |0 I:(DE-HGF)0 |k Extern |b 29 |6 P:(DE-H253)PIP1104266 |
| 910 | 1 | _ | |a European XFEL |0 I:(DE-588)1043621512 |k XFEL.EU |b 29 |6 P:(DE-H253)PIP1104266 |
| 913 | 1 | _ | |a DE-HGF |b Forschungsbereich Materie |l Großgeräte: Materie |1 G:(DE-HGF)POF4-6G0 |0 G:(DE-HGF)POF4-6G3 |3 G:(DE-HGF)POF4 |2 G:(DE-HGF)POF4-600 |4 G:(DE-HGF)POF |v PETRA III (DESY) |x 0 |
| 914 | 1 | _ | |y 2026 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0150 |2 StatID |b Web of Science Core Collection |d 2025-11-10 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1040 |2 StatID |b Zoological Record |d 2025-11-10 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1060 |2 StatID |b Current Contents - Agriculture, Biology and Environmental Sciences |d 2025-11-10 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0501 |2 StatID |b DOAJ Seal |d 2025-08-21T14:06:14Z |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1030 |2 StatID |b Current Contents - Life Sciences |d 2025-11-10 |
| 915 | _ | _ | |a Article Processing Charges |0 StatID:(DE-HGF)0561 |2 StatID |d 2025-11-10 |
| 915 | _ | _ | |a WoS |0 StatID:(DE-HGF)0113 |2 StatID |b Science Citation Index Expanded |d 2025-11-10 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1150 |2 StatID |b Current Contents - Physical, Chemical and Earth Sciences |d 2025-11-10 |
| 915 | _ | _ | |a Fees |0 StatID:(DE-HGF)0700 |2 StatID |d 2025-11-10 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0200 |2 StatID |b SCOPUS |d 2025-11-10 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1050 |2 StatID |b BIOSIS Previews |d 2025-11-10 |
| 915 | _ | _ | |a Creative Commons Attribution-NonCommercial-NoDerivs CC BY-NC-ND 4.0 |0 LIC:(DE-HGF)CCBYNCND4 |2 HGFVOC |
| 915 | _ | _ | |a JCR |0 StatID:(DE-HGF)0100 |2 StatID |b NAT COMMUN : 2022 |d 2025-11-10 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0500 |2 StatID |b DOAJ |d 2025-08-21T14:06:14Z |
| 915 | _ | _ | |a OpenAccess |0 StatID:(DE-HGF)0510 |2 StatID |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0300 |2 StatID |b Medline |d 2025-11-10 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)1190 |2 StatID |b Biological Abstracts |d 2025-11-10 |
| 915 | _ | _ | |a IF >= 15 |0 StatID:(DE-HGF)9915 |2 StatID |b NAT COMMUN : 2022 |d 2025-11-10 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0199 |2 StatID |b Clarivate Analytics Master Journal List |d 2025-11-10 |
| 915 | _ | _ | |a Peer Review |0 StatID:(DE-HGF)0030 |2 StatID |b DOAJ : Peer review |d 2025-08-21T14:06:14Z |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0160 |2 StatID |b Essential Science Indicators |d 2025-11-10 |
| 915 | _ | _ | |a DBCoverage |0 StatID:(DE-HGF)0320 |2 StatID |b PubMed Central |d 2025-11-10 |
| 920 | 1 | _ | |0 I:(DE-H253)EMBL-User-20120814 |k EMBL-User |l EMBL-User |x 0 |
| 980 | _ | _ | |a journal |
| 980 | _ | _ | |a VDB |
| 980 | _ | _ | |a UNRESTRICTED |
| 980 | _ | _ | |a I:(DE-H253)EMBL-User-20120814 |
| 980 | 1 | _ | |a FullTexts |
| Library | Collection | CLSMajor | CLSMinor | Language | Author |
|---|