Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies von Ruffolo, Jeffrey A., Chu, Lee-Shin, Mahajan, Sai Pooja, Gray, Jeffrey J.

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Antibody structure prediction using interpretable deep learning von Ruffolo, Jeffrey A., Sulam, Jeremias, Gray, Jeffrey J.

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Simultaneous prediction of antibody backbone and side-chain conformations with deep learning von Akpinaroglu, Deniz, Ruffolo, Jeffrey A, Mahajan, Sai Pooja, Gray, Jeffrey J

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Hallucinating structure-conditioned antibody libraries for target-specific binders von Mahajan, Sai Pooja, Ruffolo, Jeffrey A, Frick, Rahel, Gray, Jeffrey J

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Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen von Hutchinson, Mark, Ruffolo, Jeffrey A, Haskins, Nantaporn, Iannotti, Michael, Vozza, Giuliana, Pham, Tony, Mehzabeen, Nurjahan, Shandilya, Harini, Rickert, Keith, Croasdale-Wood, Rebecca, Damschroder, Melissa, Fu, Ying, Dippel, Andrew, Gray, Jeffrey J, Kaplan, Gilad

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Designing proteins with language models von Ruffolo, Jeffrey A., Madani, Ali

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Geometric potentials from deep learning improve prediction of CDR H3 loop structures von Ruffolo, Jeffrey A, Guerra, Carlos, Mahajan, Sai Pooja, Sulam, Jeremias, Gray, Jeffrey J

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ProGen2: Exploring the boundaries of protein language models von Nijkamp, Erik, Ruffolo, Jeffrey A., Weinstein, Eli N., Naik, Nikhil, Madani, Ali

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Flexible protein–protein docking with a multitrack iterative transformer von Chu, Lee‐Shin, Ruffolo, Jeffrey A., Harmalkar, Ameya, Gray, Jeffrey J.

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IgLM: Infilling language modeling for antibody sequence design von Shuai, Richard W., Ruffolo, Jeffrey A., Gray, Jeffrey J.

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Modeling of lamprey reticulospinal neurons: multiple distinct parameter sets yield realistic simulations von Ruffolo, Jeffrey A., McClellan, Andrew D.

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Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies von Ruffolo, Jeffrey A., Gray, Jeffrey J.

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Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer von Chu, Lee-Shin, Ruffolo, Jeffrey A, Harmalkar, Ameya, Gray, Jeffrey J

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Simultaneous prediction of antibody backbone and side-chain conformations with deep learning von Deniz Akpinaroglu, Jeffrey A. Ruffolo, Sai Pooja Mahajan, Jeffrey J. Gray

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Conditional Enzyme Generation Using Protein Language Models with Adapters von Yang, Jason, Bhatnagar, Aadyot, Ruffolo, Jeffrey A, Madani, Ali

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Deciphering antibody affinity maturation with language models and weakly supervised learning von Ruffolo, Jeffrey A, Gray, Jeffrey J, Sulam, Jeremias

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Conditional Enzyme Generation Using Protein Language Models with Adapters von Yang, Jason, Bhatnagar, Aadyot, Ruffolo, Jeffrey A, Madani, Ali

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Supplemental data for Contextual protein and antibody encodings research article von Mahajan, Sai Pooja, Ruffolo, Jeffrey A., Gray, Jeffrey A.

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Nucleases and compositions, systems, and methods thereof von Beazer, Joel, Nayfach, Stephen, Bhatnagar, Aadyot, Madani, Ali, Ruffolo, Jeffrey A

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Deciphering antibody affinity maturation with language models and weakly supervised learning von Ruffolo, Jeffrey A, Gray, Jeffrey J, Sulam, Jeremias

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