| Deep learning in protein structural modeling and design W Gao, SP Mahajan, J Sulam, JJ Gray Patterns 1 (9), 2020 | 199 | 2020 |
| Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies JA Ruffolo, LS Chu, SP Mahajan, JJ Gray Nature communications 14 (1), 2389, 2023 | 91 | 2023 |
| Geometric potentials from deep learning improve prediction of CDR H3 loop structures JA Ruffolo, C Guerra, SP Mahajan, J Sulam, JJ Gray Bioinformatics 36 (Supplement_1), i268-i275, 2020 | 63 | 2020 |
| Computational affinity maturation of camelid single-domain intrabodies against the nonamyloid component of alpha-synuclein SP Mahajan, B Meksiriporn, D Waraho-Zhmayev, KB Weyant, I Kocer, ... Scientific reports 8 (1), 17611, 2018 | 40 | 2018 |
| The structure of the colorectal cancer-associated enzyme GalNAc-T12 reveals how nonconserved residues dictate its function AJ Fernandez, EJP Daniel, SP Mahajan, JJ Gray, TA Gerken, LA Tabak, ... Proceedings of the National Academy of Sciences 116 (41), 20404-20410, 2019 | 20 | 2019 |
| Hallucinating structure-conditioned antibody libraries for target-specific binders SP Mahajan, JA Ruffolo, R Frick, JJ Gray Frontiers in immunology 13, 999034, 2022 | 15 | 2022 |
| Tilting the balance between canonical and noncanonical conformations for the H1 hypervariable loop of a llama VHH through point mutations SP Mahajan, C Velez-Vega, FA Escobedo The Journal of Physical Chemistry B 117 (1), 13-24, 2013 | 10 | 2013 |
| Induced fit with replica exchange improves protein complex structure prediction A Harmalkar, SP Mahajan, JJ Gray PLoS computational biology 18 (6), e1010124, 2022 | 8 | 2022 |
| Simultaneous prediction of antibody backbone and side-chain conformations with deep learning D Akpinaroglu, JA Ruffolo, SP Mahajan, JJ Gray PloS one 17 (6), e0258173, 2022 | 6 | 2022 |
| Improved antibody structure prediction by deep learning of side chain conformations D Akpinaroglu, JA Ruffolo, SP Mahajan, JJ Gray BioRxiv, 2021.09. 22.461349, 2021 | 6 | 2021 |
| Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2 SP Mahajan, Y Srinivasan, JW Labonte, MP DeLisa, JJ Gray ACS catalysis 11 (5), 2977-2991, 2021 | 5 | 2021 |
| Contextual protein and antibody encodings from equivariant graph transformers SP Mahajan, JA Ruffolo, JJ Gray bioRxiv, 2023 | 1 | 2023 |
| Exploiting language models for protein discovery with latent walk-jump sampling SP Mahajan, NC Frey, D Berenberg, J Kleinhenz, R Bonneau, ... Machine Learning for Structural Biology Workshop, NeurIPS, 2023 | 1 | 2023 |
| Towards deep learning models for target-specific antibody design SP Mahajan, J Ruffolo, R Frick, JJ Gray Biophysical Journal 121 (3), 528a, 2022 | 1 | 2022 |
| NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries EM Nowara, PO Pinheiro, SP Mahajan, O Mahmood, AM Watkins, ... arXiv preprint arXiv:2407.03428, 2024 | | 2024 |
| Discovery of a single-subunit oligosaccharyltransferase that enables glycosylation of full-length IgG antibodies in Escherichia coli B Sotomayor, TC Donahue, SP Mahajan, MN Taw, SW Hulbert, ... bioRxiv, 2024.08. 12.607630, 2024 | | 2024 |
| Track: Machine Learning in Protein Science Hallucinating native-like antibodies with deep learning SP Mahajan, JA Ruffolo, R Frick, JJ Gray PROTEIN SCIENCE 32, 2023 | | 2023 |
| Context-Aware Representations from Deep Learning for Antibody Design SP Mahajan, JJ Gray 2022 AIChE Annual Meeting, 2022 | | 2022 |
| Hallucinating Inexpensive, Diverse and Native-like Antibody Binders with Deep Learning SP Mahajan, J Ruffolo, R Frick, JJ Gray 2022 AIChE Annual Meeting, 2022 | | 2022 |
| Exploring Antibody Design Space with Deep Learning Models SP Mahajan 2022 AIChE Annual Meeting, 2022 | | 2022 |
