Bibliography#

1

Mohammad Shoeybi, Mostofa Patwary, Raul Puri, Patrick LeGresley, Jared Casper, and Bryan Catanzaro. Megatron-lm: training multi-billion parameter language models using model parallelism. CoRR, 2019. URL: http://arxiv.org/abs/1909.08053, arXiv:1909.08053.

2

Deepak Narayanan, Mohammad Shoeybi, Jared Casper, Patrick LeGresley, Mostofa Patwary, Vijay Korthikanti, Dmitri Vainbrand, Prethvi Kashinkunti, Julie Bernauer, Bryan Catanzaro, Amar Phanishayee, and Matei Zaharia. Efficient large-scale language model training on GPU clusters. CoRR, 2021. URL: https://arxiv.org/abs/2104.04473, arXiv:2104.04473.

3

Jared Kaplan, Sam McCandlish, Tom Henighan, Tom B. Brown, Benjamin Chess, Rewon Child, Scott Gray, Alec Radford, Jeffrey Wu, and Dario Amodei. Scaling laws for neural language models. CoRR, 2020. URL: https://arxiv.org/abs/2001.08361, arXiv:2001.08361.

4

Christian Dallago, Jody Mou, Kadina E. Johnston, Bruce J. Wittmann, Nicholas Bhattacharya, Samuel Goldman, Ali Madani, and Kevin K. Yang. Flip: benchmark tasks in fitness landscape inference for proteins. 2022. doi:10.1101/2021.11.09.467890.

5

Octavian-Eugen Ganea, Xinyuan Huang, Charlotte Bunne, Yatao Bian, Regina Barzilay, Tommi Jaakkola, and Andreas Krause. Independent se (3)-equivariant models for end-to-end rigid protein docking. arXiv preprint arXiv:2111.07786, 2021.

6

Martin Buttenschoen, Garrett M. Morris, and Charlotte M. Deane. Posebusters: ai-based docking methods fail to generate physically valid poses or generalise to novel sequences. 2023. arXiv:2308.05777.

7

Thom Vreven, Iain H Moal, Anna Vangone, Brian G Pierce, Panagiotis L Kastritis, Mieczyslaw Torchala, Raphael Chaleil, Brian Jiménez-García, Paul A Bates, Juan Fernandez-Recio, and others. Updates to the integrated protein–protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2. Journal of molecular biology, 427(19):3031–3041, 2015.

8

Raphael Townshend, Rishi Bedi, Patricia Suriana, and Ron Dror. End-to-end learning on 3d protein structure for interface prediction. Advances in Neural Information Processing Systems, 2019.

9

missing journal in robin2023automated

10

Gustaf Ahdritz, Nazim Bouatta, Christina Floristean, Sachin Kadyan, Qinghui Xia, William Gerecke, Timothy J O\textquoteright Donnell, Daniel Berenberg, Ian Fisk, Niccolò Zanichelli, Bo Zhang, Arkadiusz Nowaczynski, Bei Wang, Marta M Stepniewska-Dziubinska, Shang Zhang, Adegoke Ojewole, Murat Efe Guney, Stella Biderman, Andrew M Watkins, Stephen Ra, Pablo Ribalta Lorenzo, Lucas Nivon, Brian Weitzner, Yih-En Andrew Ban, Peter K Sorger, Emad Mostaque, Zhao Zhang, Richard Bonneau, and Mohammed AlQuraishi. OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization. bioRxiv, 2022. URL: https://www.biorxiv.org/content/10.1101/2022.11.20.517210, arXiv:https://www.biorxiv.org/content/early/2022/11/22/2022.11.20.517210.full.pdf, doi:10.1101/2022.11.20.517210.