Jeffrey A. Ruffolo

MedicineBiochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 17 papers. Top paper: “Geometric potentials from deep learning improve prediction of CDR H3 loop structures”.

Geometric potentials from deep learning improve prediction of CDR H3 loop structures

Bioinformatics(2020)10.1093/bioinformatics/btaa457

N/A

0DataRank · unranked

83 citations

Carlos Guerra, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray, Jeffrey A. Ruffolo

Geometric Potentials from Deep Learning Improve Prediction of CDR H3 Loop Structures

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.09.940254

N/A

0DataRank · unranked

8 citations

Carlos Guerra, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray, Jeffrey A. Ruffolo

Antibody structure prediction using interpretable deep learning

Patterns(2021)10.1016/j.patter.2021.100406

N/A

0DataRank · unranked

214 citations

Jeremias Sulam, Jeffrey J. Gray, Jeffrey A. Ruffolo

Generative language modeling for antibody design

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.13.472419

N/A

0DataRank · unranked

48 citations

Jeffrey A. Ruffolo, Jeffrey J. Gray, Richard W. Shuai

Antibody structure prediction using interpretable deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.27.445982

N/A

0DataRank · unranked

22 citations

Jeremias Sulam, Jeffrey J. Gray, Jeffrey A. Ruffolo

Improved antibody structure prediction by deep learning of side chain conformations

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.22.461349

N/A

0DataRank · unranked

4 citations

Jeffrey A. Ruffolo, Sai Pooja Mahajan, Jeffrey J. Gray, Deniz Akpinaroglu

Hallucinating structure-conditioned antibody libraries for target-specific binders

Frontiers in Immunology(2022)10.3389/fimmu.2022.999034

N/A

0DataRank · unranked

21 citations

Jeffrey A. Ruffolo, Rahel Frick, Jeffrey J. Gray, Sai Pooja Mahajan

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

PLoS ONE(2022)10.1371/journal.pone.0258173

N/A

0DataRank · unranked

16 citations

Jeffrey A. Ruffolo, Sai Pooja Mahajan, Jeffrey J. Gray, Deniz Akpinaroglu

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.20.488972

N/A

0DataRank · unranked

35 citations

Lee‐Shin Chu, Sai Pooja Mahajan, Jeffrey J. Gray, Jeffrey A. Ruffolo

Hallucinating structure-conditioned antibody libraries for target-specific binders

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.06.494991

N/A

0DataRank · unranked

1 citations

Jeffrey A. Ruffolo, Rahel Frick, Jeffrey J. Gray, Sai Pooja Mahajan

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

Nature Communications(2023)10.1038/s41467-023-38063-x

N/A

0DataRank · unranked

317 citations

Lee‐Shin Chu, Sai Pooja Mahajan, Jeffrey J. Gray, Jeffrey A. Ruffolo

IgLM: Infilling language modeling for antibody sequence design

Cell Systems(2023)10.1016/j.cels.2023.10.001

N/A

0DataRank · unranked

128 citations

Jeffrey A. Ruffolo, Jeffrey J. Gray, Richard W. Shuai

Flexible protein–protein docking with a multitrack iterative transformer

Protein Science(2023)10.1002/pro.4862

N/A

0DataRank · unranked

32 citations

Jeffrey A. Ruffolo, Ameya Harmalkar, Jeffrey J. Gray, Lee‐Shin Chu

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.29.547134

N/A

0DataRank · unranked

7 citations

Jeffrey A. Ruffolo, Ameya Harmalkar, Jeffrey J. Gray, Lee‐Shin Chu

Contextual protein and antibody encodings from equivariant graph transformers

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.15.549154

N/A

0DataRank · unranked

4 citations

Jeffrey A. Ruffolo, Jeffrey J. Gray, Sai Pooja Mahajan

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

mAbs(2024)10.1080/19420862.2024.2362775

N/A

0DataRank · unranked

17 citations

Jeffrey A. Ruffolo, Nantaporn Haskins, Michael J. Iannotti, Giuliana Vozza, Tony Pham +10 more

How well do contextual protein encodings learn structure, function, and evolutionary context?

Cell Systems(2025)10.1016/j.cels.2025.101201

N/A

0DataRank · unranked

0 citations

Fátima A. Dávila-Hernández, Jeffrey A. Ruffolo, Jeffrey J. Gray, Sai Pooja Mahajan