Updated publications

Author: amjjbonvin

publications/index.md

@@ -8,7 +8,7 @@ image:
 
 * M. Sánchez-Marín,  M. Giuliniand **A.M.J.J. Bonvin**. [Combining AI structure prediction and integrative modelling for nanobody-antigen complexes](https://doi.org/10.1101/2025.07.01.662355). _BioRxiv_ 10.1101/2025.07.01.662355 (2025).
 
-* A. Kryshtafovych, M. Milostan, M. Lensink, S. Velankar, **A.M.J.J. Bonvin**, J. Moult and K. Fidelis. [Updates to the CASP infrastructure in 2024](https://doi.org/10.22541/au.174646994.49522644/v1). _Authorea_ 10.22541/au.174646994.49522644/v1 (2025) 
+* A. Kryshtafovych, M. Milostan, M. Lensink, S. Velankar, **A.M.J.J. Bonvin**, J. Moult and K. Fidelis. Updates to the CASP infrastructure in 2024. _Proteins: Struc. Funct. & Bioinformatics_. In press (2025). Preprint [here](https://doi.org/10.22541/au.174646994.49522644/v1)
 
 * M. Lensink, N. Raouraoua, G. Brysbaert, S. Velankar, S. Wodak and **A.M.J.J. Bonvin**. [Protein-protein interaction prediction in the pre- and
 post-AlphaFold era: the 8th CAPRI evaluation](http://doi.org/10.1002/prot.70018). _Proteins: Struc. Funct. & Bioinformatics_.  Advanced Online Publication DOI:10.1002/prot.70018 (2025)
@@ -37,7 +37,7 @@ Jimenez-Garcia, Z. Jandova, P.I. Koukos, C. van Noort, J.M. . Teixeira, S.C. van
 
 * M. Giulini, C. Schneider, D. Cutting, N. Desai, C. Deane and **A.M.J.J. Bonvin**. [Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking](https://doi.org/10.1093/bioinformatics/btae583). _Bioinformatics_ *40*:btae583, p. 1-11 (2024).[BioRxiv](https://www.biorxiv.org/content/10.1101/2023.11.17.567543v1)
 
-* R.V. Honorato, M.E. Trellet, B. Jiménez-García1, J.J. Schaarschmidt, M. Giulini, V. Reys,  P.I. Koukos, J.P.G.L.M. Rodrigues, E. Karaca, G.C.P. van Zundert, J. Roel-Touris, C.W. van Noort, Z. Jandová, A.S.J. Melquiond and **A.M.J.J. Bonvin**. [The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes](https://www.nature.com/articles/s41596-024-01011-0.epdf?sharing_token=UHDrW9bNh3BqijxD2u9Xd9RgN0jAjWel9jnR3ZoTv0O8Cyf_B_3QikVaNIBRHxp9xyFsQ7dSV3t-kBtpCaFZWPfnuUnAtvRG_vkef9o4oWuhrOLGbBXJVlaaA9ALOULn6NjxbiqC2VkmpD2ZR_r-o0sgRZoHVz10JqIYOeus_nM%3D). _Nature Prot._, *19*, 3219–3241 (2024).
+* R.V. Honorato, M.E. Trellet, B. Jiménez-García1, J.J. Schaarschmidt, M. Giulini, V. Reys,  P.I. Koukos, J.P.G.L.M. Rodrigues, E. Karaca, G.C.P. van Zundert, J. Roel-Touris, C.W. van Noort, Z. Jandová, A.S.J. Melquiond and **A.M.J.J. Bonvin**. [The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes](https://www.nature.com/articles/s41596-024-01011-0.epdf?sharing_token=UHDrW9bNh3BqijxD2u9Xd9RgN0jAjWel9jnR3ZoTv0O8Cyf_B_3QikVaNIBRHxp9xyFsQ7dSV3t-kBtpCaFZWPfnuUnAtvRG_vkef9o4oWuhrOLGbBXJVlaaA9ALOULn6NjxbiqC2VkmpD2ZR_r-o0sgRZoHVz10JqIYOeus_nM%3D). _Nature Prot._, *19*, 3219–3241 (2024). Open access version [here](https://research-portal.uu.nl/ws/portalfiles/portal/245780710/s41596-024-01011-0_1_.pdf)
 
 * B. Vallat, B.M. Webb, J.D. Westbrook, T. Goddard, C.A. Hanke, A. Graziadei, E. Peisach, A. Zalevsky, J. Sagendorf, H. Tangmunarunkit, S. Voinea, M. Sekharan, J. Yu, **A.M.J.J. Bonvin**, Fr, DiMaio, G. Hummer, J. Meiler, E. Tajkhorshid, T. Ferrin, C.L. Lawson, A. Leitner, J. Rappsilber, C.A.M. Seidel, C.M. Jeffries, S.K. Burley, J. Hoch, G.i Kurisu, K.e Morris, A. Patwardhan, S. Velankar, T. Schwede, J. Trewhella, C. Kesselman, H.M. Berman, A. Sali. [IHMCIF: An extension of PDBx/mmCIF data standard for integrative structure determination methods](https://doi.org/10.1016/j.jmb.2024.168546). _J. Mol. Biol._, *436*:168546 (2024).