Ruffolo, Jeffrey A.

ProGen2: Exploring the boundaries of protein language models

Nijkamp, E., Ruffolo, J. A., Weinstein, E. N., Naik, N., & Madani, A. (2023) · Cell Systems

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 480

Antibody structure prediction using interpretable deep learning

Ruffolo, J. A., Sulam, J., & Gray, J. J. (2022) · Patterns

Protein Structure and DynamicsMonoclonal and Polyclonal Antibodies Research

Cited by 216

Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences

Ruffolo, J. A., Nayfach, S., Gallagher, J., Bhatnagar, A., Beazer, J., Hussain, R., Russ, J., Yip, J., Hill, E., Pacesa, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

CRISPR and Genetic EngineeringRNA regulation and disease

Cited by 90

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer

Chu, L.-S., Ruffolo, J. A., Harmalkar, A., & Gray, J. J. (2023) · Protein Science

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 42

Flexible protein–protein docking with a multitrack iterative transformer

Chu, L., Ruffolo, J. A., Harmalkar, A., & Gray, J. J. (2024) · Protein Science

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 41

Enhancement of antibody thermostability and affinity by computational design in the absence of antigen

Hutchinson, M., Ruffolo, J. A., Haskins, N., Iannotti, M., Vozza, G., Pham, T., Mehzabeen, N., Shandilya, H., Rickert, K., Croasdale-Wood, R., et al. (2023) · mAbs

Monoclonal and Polyclonal Antibodies Researchvaccines and immunoinformatics approaches

Cited by 22

Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen

Hutchinson, M., Ruffolo, J. A., Haskins, N., Iannotti, M., Vozza, G., Pham, T., Mehzabeen, N., Shandilya, H., Rickert, K., Croasdale-Wood, R., et al. (2024) · mAbs

Monoclonal and Polyclonal Antibodies Researchvaccines and immunoinformatics approaches

Cited by 22

Simultaneous prediction of antibody backbone and side-chain conformations with deep learning

Akpinaroglu, D., Ruffolo, J. A., Mahajan, S. P., & Gray, J. J. (2022) · PLOS ONE

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 21

Hallucinating structure-conditioned antibody libraries for target-specific binders

Mahajan, S. P., Ruffolo, J. A., Frick, R., & Gray, J. J. (2022) · Frontiers in Immunology

Monoclonal and Polyclonal Antibodies Researchvaccines and immunoinformatics approaches

Cited by 20

Contextual protein and antibody encodings from equivariant graph transformers

Mahajan, S. P., Ruffolo, J. A., & Gray, J. J. (2023) · Cell Systems

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 3