Skip to content

Commit

Permalink
Updated publications
Browse files Browse the repository at this point in the history
  • Loading branch information
@amjjbonvin
amjjbonvin committed Oct 1, 2024
1 parent 2ab65d3 commit f7aa90a
Showing 1 changed file with 7 additions and 5 deletions.
12 changes: 7 additions & 5 deletions publications/index.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,17 +5,21 @@ image:
feature: pages/banner_publications-mini.jpg
---
## 2024
* V. Reys∗, Ma. Giulini∗, V. Cojocaru, A. Engel, X. Xu, J. Roel-Touris, C. Geng, F. Ambrosetti, B.
Jimenez-Garcia, Z. Jandova, P.I. Koukos, C. van Noort, J.M. . Teixeira, S.C. van Keulen, M. Reau, R.V. Honorato and **A.M.J.J. Bonvin**. [Integrative modeling in the age of machine learning: a summary of HADDOCK strategies in CAPRI rounds 47-55](https://doi.org/10.1101/2024.09.16.613212) _BioRXiv._ (2024).

* K. Devantier, T.L. Toft-Bertelsen, A. Prestel, V.M.S. Kjaer, C.a Sahin, M. Giulini, S. Louka, K. Spiess, A. Manandhar, K. Qvortrup, T. Ulven, B. Hjorth Bentzen, **A.M.J.J. Bonvin**, N. MacAulay, B.B. Kragelund and M.M. Rosenkilde. [The SH Protein of Mumps Virus is a Druggable Pentameric Viroporin](https://doi.org/10.1101/2024.08.09.60700). _BioRXiv._ 10.1101/2024.08.09.60700 (2024).

* A. Ranaudo, M. Giulini, A. Pelissou Ayuso and **A.M.J.J. Bonvin**. [Modelling Protein-Glycan Interactions with HADDOCK](https://doi.org/10.1101/2024.07.31.605986). _BioRXiv._ 10.1101/2024.07.31.605986 (2024).

* X. Xu and **A.M.J.J. Bonvin** [Ranking protein-protein models with large language models and graph neural networks](https://arxiv.org/abs/2407.16375). _arXiv_:2407.16375 (2024).

* G. Bellinzona, D. Sassera and **A.M.J.J. Bonvin**. [Accelerating Protein-Protein Interaction screens with reduced AlphaFold-Multimer sampling](https://www.biorxiv.org/content/10.1101/2024.06.07.597882v2) _BioRXiv_ 10.1101/2024.06.07.597882 (2024).

* A. Basciu, M. Athar, H. Kurt, C. Neville, G. Malloci, F. Muredda, A. Bosin, P. Ruggerone, **A.M.J.J. Bonvin** and A.V. Vargiu. [Predicting binding events in very flexible, allosteric, multi-domain proteins](https://doi.org/10.1101/2024.06.02.597018). _BioRXiv._ 10.1101/2024.06.02.597018 (2024).

* A. Ranaudo, M. Giulini, A. Pelissou Ayuso and **A.M.J.J. Bonvin**. [Modelling Protein-Glycan Interactions with HADDOCK](https://doi.org/10.1101/2024.07.31.605986). _J. Chem. Inf. Mod._ In press (2024). [BioRXiv](https://doi.org/10.1101/2024.07.31.605986)

* 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_ Advanced Online Publication, 10.1093/bioinformatics/btae583 (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._, Advanced Online Publication DOI: 10.1038/s41596-024-01011-0 (2024).

* 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).
Expand All @@ -24,13 +28,11 @@ image:

* M. Giulini, R.V. Honorato, J.L. Rivera, **A.M.J.J. Bonvin**. [ARCTIC-3D: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information](https://doi.org/10.1038/s42003-023-05718-w). _Comm. Biol._ *7*:49, p. 1-9 (2024).

* X. Xu, **A.M.J.J. Bonvin**. [DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model](https://doi.org/10.1093/bioadv/vbad191). _Bioinfo. Adv._ *4*:vbad191 (2024).
* X. Xu, **A.M.J.J. Bonvin**. [DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model](https://doi.org/10.1093/bioadv/vbad191). _Bioinfo. Adv._ vbad191, _Advanced Online Publication (2024).


## 2023

* 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://www.biorxiv.org/content/10.1101/2023.11.17.567543v1). _BioRXiv._ 10.1101/2023.11.17.567543v1 (2023).

* **A.M.J.J. Bonvin**. [Empowering Global Collaboration in Structural Biology and Life Sciences](https://zenodo.org/record/8135315). DOI:10.5281/zenodo.8135315 (2023).

* M. Lensink, G. Brysbaert, N. Raouraoua, P. Bates, M. Giulini, R. Vargas Honorato, C. van Noort, J. Teixeira, **A.M.J.J. Bonvin**, R. Kong, H. Shi, X. Lu, S. Chang, J. Liu, Z. Guo, X. Chen, A. Morehead, R. Roy, T. Wu, N. Giri, F. Quadir, C. Chen, J. Cheng, C. Del Carpio, E. Ichiishi, L. Rodriguez-Lumbreras, J. Fernández-Recio, A. Harmalkar, L. Chu, S.Canner, R. Smanta, J. Gray, H. Li, P. Lin, J.a He, H. Tao, S. Huang, J. Roel, B. Jimenez-Garcia, C. Christoffer, A. Jain J, Y. Kagaya, H. Kannan, T. Nakamura, G. Terashi, J. Verburgt, Y. Zhang, Z. Zhang, H. Fujuta, M. Sekijima, D. Kihara, O. Khan, S. Kotelnikov, U. Ghani, D. Padhorny, D. Beglov, S. Vajda, D. Kozakov, S. Negi S, T. Ricciardelli, D. Barradas-Bautista, Z. Cao, M. Chawla, L. Cavallo, R. Oliva, R. Yin, M. Cheung, J. Guest, J. Lee, B. Pierce, B. Shor, T. Cohen, M. Halfon, D. Schneidman-Duhovny, S. Zhu, R. Yin, Y. Sun, Y. Shen, M. Maszota-Zieleniak, K. Bojarski K, E. Lubecka, M. Marcisz, A. Danielsson, L. Dziadek, M. Gaardlos, A. Giełdoń, J. Liwo, S. Samsonov, R. Slusarz, K. Zieba, A. Sieradzan, C. Czaplewski , S. Kobayashi, Y. Miyakawa, Y. Kiyota, M. Takeda-Shitaka, K. Olechnovič, L. Valančauskas, J. Dapkūnas, C. Venclovas, B. Wallner, L. Yang, C. Hou, X. He, S. Guo, S. Jiang, X. Ma, R. Duan, L. Qiu, X. Xu, X. Zou, S. Velankar, S. Wodak. [Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment](https://doi.org/10.1002/prot.26609) _Proteins: Struc. Funct. & Bioinformatics_ *12*, 1658-1683 (2023).
Expand Down

0 comments on commit f7aa90a

Please sign in to comment.