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J

Jeffrey J. Gray

johns hopkins university

70H-index
388Paper Count
2.2WCitation Count
Published Papers 117
Publication Date
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A blinded, prospective benchmark of in silico antibody discovery anchored to experimental affinity and developability
errNature Biotechnology
IF41.7
err2026-08-19
err0
errOAAI
errM. Frank Erasmus; Daniel Bedinger; Elizabeth Hopkins; Ginger Ferguson; Justine Strickler; Christilyn P. Graff; Samantha R. Summers; Stacy L. Capehart; Joshua D. Slocum; Crystal Richardson; Sumit Kumar; Zhifei Sun; Yujie Shang; Jixian Zhang; Ming Gu; Lixia Yi; Alon Wellner; Shuangjia Zheng; Wei Lu; Pietro Sormanni; Matthew Greenig; Haiping Zhang; Brendan T. Mann; Mahdi Baghbanzadeh; Ali Rahnavard; Gregory L. Moore; Huaiyu Sun; Ying Ding; Alex Nisthal; Jitendra Kanodia; Matthew J. Bernett; Aurélien Pélissier; Yanjun Shao; Maria Rodriguez Martinez; Karthik Ramesh; Horacio Nastri; Andreas Evers; Anhar Abdelatif; Andrew J. Bordner; Mykola Bordyuh; Lim Heo; Brian A. Kidd; H. Serhat Tetikol; Shuai Wei; Jung-Eun Shin; Ryan Peckner; Leigh Manley; Ajitesh Lunge; Yashas Devasurmutt; Bora Guloglu; Liviu Copoiu; Miles McGibbon; Monica L. Fernandez-Quintero; Nitesh Mishra; Sean M. Callaghan; Olivia M. Swanson; Daniel L. V. Bader; James A. Ferguson; Sai S. R. Raghavan; Benjamin Nemoz; Colleen A. Maillie; Charles Bowman; Bryan Briney; Andrew B. Ward; Paolo Marcatili; Rahmad Akbar; Bing He; Fandi Wu; Jianhua Yao; Bin Hu; Michal Kucer; Kaetlyn Rose Gibson; Rahul Somasundaram; Li-Wei Hung; Tomasz Kaszuba; Daved H. Fremont; Hyeongsun Jeong; Vinodh Babu Kurella; Shipra Malhotra; Satyendra Kumar; Yanyun Liu; Lingling Xu; Joshua Misa; Alexander Nicholas St. John; Jeff Vogt; Fátima A. Dávila-Hernández; Da Xu; Michael Chungyoun; Zyaja D. Huggan; Jeffrey J. Gray; Jonathan Parkinson; Young Su Ko; Wei Wang; Franziska Geiger; Jonathon D. Ziegler; Nikhil Haas; Chance Challacombe; Ahmad Qamar; Akshita Singh; Yi-Ching Tang; Zhiqiang An; Xiaoqian Jiang; Yejin Kim; Xinyan Zhao; Erik Swanson; Jürgen Klattig; Karsten Winkler; Tschimegma Bataa; Volker Sandig; Lilian Denzler; Chunan Liu; Randall J. Brezski; Laura Spector; Katheryn Perea-Schmittle; Sara D’Angelo; Fortunato Ferrara; Andrew R. M. Bradbury
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The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling
errJournal of Chemical Information and Modeling
IF5.3
err2026-03-10
err0
PREAI
errKarmen Čondić-Jurkić; Irfan Alibay; Woody Sherman; Mallory R. Tollefson; W. Patrick Walters; Zachary Baker; Lillian T. Chong; Jennifer N. Wei; Jeffrey Gray; Brian D. Weitzner; Daniel G. A. Smith; Julia Koehler Leman; Chris Bahl; David L. Mobley
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errSave
Docking With Rosetta and Deep Learning Approaches in CAPRI Rounds 47-55
errPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
IF2.8
err2025-09-01
err0
errOAAI
errHarmalkar, Ameya; Chu, Lee-Shin; Canner, Samuel W.; Samanta, Rituparna; Frick, Rahel; Davila-Hernandez, Fatima A.; Sarma, Sudeep; Hitawala, Fatima; Gray, Jeffrey J.
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errSave
What does AlphaFold3 learn about antibody and nanobody docking, and what remains unsolved?
errmAbs
IF7.3
err2025-08-14
err0
errOAAI
errFatima N. Hitawala; Jeffrey J. Gray
errShare
errSave
Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides
errMOLECULAR & CELLULAR PROTEOMICS
IF5.5
err2025-02-01
err0
errOAAI
errHsiao, Meng-Hsuan; Miao, Yang; Liu, Zixing; Schutze, Konstantin; Limjunyawong, Nathachit; Chien, Daphne Chun-Che; Monteiro, Wayne Denis; Chu, Lee-Shin; Morgenlander, William; Jayaraman, Sahana; Jang, Sung-eun; Gray, Jeffrey J.; Zhu, Heng; Dong, Xinzhong; Steinegger, Martin; Larman, H. Benjamin
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errSave
Advancing Membrane-Associated Protein Docking with Improved Sampling and Scoring in Rosetta
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2024-11-22
err0
PREAI
errSamanta, Rituparna; Harmalkar, Ameya; Prathima, Priyamvada; Gray, Jeffrey J.
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errSave
Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen
errMABS
IF7.3
err2024-06-20
err2
errOAAI
errHutchinson, 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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The Human Ganglioside Interactome in Live Cells Revealed Using Clickable Photoaffinity Ganglioside Probes
errJOURNAL OF THE AMERICAN CHEMICAL SOCIETY
IF15.6
err2024-06-18
err3
PREAI
errZhang, Gao-Lan; Porter, Mitchell J.; Awol, Abduselam K.; Orsburn, Benjamin C.; Canner, Samuel W.; Gray, Jeffrey J.; O'Meally, Robert N.; Cole, Robert N.; Schnaar, Ronald L.
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errSave
Thermostability Enhancement of GH 62 α-l-Arabinofuranosidase by Directed Evolution and Rational Design
errJOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
IF6.2
err2024-02-14
err4
PREAI
errMartins, Manoela; dos Santos, Alberto M.; da Costa, Clauber H. S.; Canner, Samuel W.; Chungyoun, Michael; Gray, Jeffrey J.; Skaf, Munir S.; Ostermeier, Marc; Goldbeck, Rosana
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errSave
IgLM: Infilling language modeling for antibody sequence design
errCELL SYSTEMS
IF7.7
err2023-11-01
err20
errOAAI
errShuai, Richard W.; Ruffolo, Jeffrey A.; Gray, Jeffrey J.
errShare
errSave
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
errPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
IF2.8
err2023-10-31
err33
errOAAI
errLensink, Marc F.; Brysbaert, Guillaume; Raouraoua, Nessim; Bates, Paul A.; Giulini, Marco; Honorato, Rodrigo V.; van Noort, Charlotte; Teixeira, Joao M. C.; Bonvin, Alexandre M. J. J.; Kong, Ren; Shi, Hang; Lu, Xufeng; Chang, Shan; Liu, Jian; Guo, Zhiye; Chen, Xiao; Morehead, Alex; Roy, Raj S.; Wu, Tianqi; Giri, Nabin; Quadir, Farhan; Chen, Chen; Cheng, Jianlin; Del Carpio, Carlos A.; Ichiishi, Eichiro; Rodriguez-Lumbreras, Luis A.; Fernandez-Recio, Juan; Harmalkar, Ameya; Chu, Lee-Shin; Canner, Sam; Smanta, Rituparna; Gray, Jeffrey J.; Li, Hao; Lin, Peicong; He, Jiahua; Tao, Huanyu; Huang, Sheng-You; Roel-Touris, Jorge; Jimenez-Garcia, Brian; Christoffer, Charles W.; Jain, Anika J.; Kagaya, Yuki; Kannan, Harini; Nakamura, Tsukasa; Terashi, Genki; Verburgt, Jacob C.; Zhang, Yuanyuan; Zhang, Zicong; Fujuta, Hayato; Sekijima, Masakazu; Kihara, Daisuke; Khan, Omeir; Kotelnikov, Sergei; Ghani, Usman; Padhorny, Dzmitry; Beglov, Dmitri; Vajda, Sandor; Kozakov, Dima; Negi, Surendra S.; Ricciardelli, Tiziana; Barradas-Bautista, Didier; Cao, Zhen; Chawla, Mohit; Cavallo, Luigi; Oliva, Romina; Yin, Rui; Cheung, Melyssa; Guest, Johnathan D.; Lee, Jessica; Pierce, Brian G.; Shor, Ben; Cohen, Tomer; Halfon, Matan; Schneidman-Duhovny, Dina; Zhu, Shaowen; Yin, Rujie; Sun, Yuanfei; Shen, Yang; Maszota-Zieleniak, Martyna; Bojarski, Krzysztof K.; Lubecka, Emilia A.; Marcisz, Mateusz; Danielsson, Annemarie; Dziadek, Lukasz; Gaardlos, Margrethe; Gieldon, Artur; Liwo, Adam; Samsonov, Sergey A.; Slusarz, Rafal; Zieba, Karolina; Sieradzan, Adam K.; Czaplewski, Cezary; Kobayashi, Shinpei; Miyakawa, Yuta; Kiyota, Yasuomi; Takeda-Shitaka, Mayuko; Olechnovic, Kliment; Valancauskas, Lukas; Dapkunas, Justas; Venclovas, Ceslovas; Wallner, Bjorn; Yang, Lin; Hou, Chengyu; He, Xiaodong; Guo, Shuai; Jiang, Shenda; Ma, Xiaoliang; Duan, Rui; Qui, Liming; Xu, Xianjin; Zou, Xiaoqin; Velankar, Sameer; Wodak, Shoshana J.
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errSave
Fate and Efficacy of Engineered Allogeneic Stem Cells Targeting Cell Death and Proliferation Pathways in Primary and Brain Metastatic Lung Cancer
errSTEM CELLS TRANSLATIONAL MEDICINE
IF4.9
err2023-06-13
err2
errOAAI
errMoleirinho, Susana; Kitamura, Yohei; Borges, Paulo S. G. N.; Auduong, Sophia; Kilic, Seyda; Deng, David; Kanaya, Nobuhiko; Kozono, David; Zhou, Jing; Gray, Jeffrey J.; Revai-Lechtich, Esther; Zhu, Yanni; Shah, Khalid
errShare
errSave
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
errNATURE COMMUNICATIONS
IF15.7
err2023-04-25
err76
errOAAI
errRuffolo, Jeffrey A.; Chu, Lee-Shin; Mahajan, Sai Pooja; Gray, Jeffrey J.
errShare
errSave
Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features
errMABS
IF7.3
err2023-01-22
err12
errOAAI
errHarmalkar, Ameya; Rao, Roshan; Xie, Yuxuan Richard; Honer, Jonas; Deisting, Wibke; Anlahr, Jonas; Hoenig, Anja; Czwikla, Julia; Sienz-Widmann, Eva; Rau, Doris; Rice, Austin J.; Riley, Timothy P.; Li, Danqing; Catterall, Hannah B.; Tinberg, Christine E.; Gray, Jeffrey J.; Wei, Kathy Y.
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errSave
Hallucinating structure-conditioned antibody libraries for target-specific binders
errFRONTIERS IN IMMUNOLOGY
IF5.9
err2022-10-21
err9
errOAAI
errMahajan, Sai Pooja; Ruffolo, Jeffrey A.; Frick, Rahel; Gray, Jeffrey J.
errShare
errSave
De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)
errPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
IF2.8
err2022-10-08
err7
errOAAI
errBoorla, Veda Sheersh; Chowdhury, Ratul; Ramasubramanian, Ranjani; Ameglio, Brandon; Frick, Rahel; Gray, Jeffrey J.; Maranas, Costas D.
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Understanding the interactions between bone mineral crystals and their binding peptides derived from filamentous phage
errMATERIALS TODAY ADVANCES
IF8
err2022-08-01
err7
errOAAI
errLi, Yan; Cao, Binrui; Modali, Sita; Lee, Elizabeth M. Y.; Xu, Hong; Petrenko, Valery; Gray, Jeffrey J.; Yang, Mingying; Mao, Chuanbin
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errSave
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design (vol 13, pg 3031, 2017)
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2022-06-06
err5
PREAI
errAlford, Rebecca F.; Leaver-Fay, Andrew; Jeliazkov, Jeliazko R.; O'Meara, Matthew J.; DiMaio, Frank P.; Park, Hahnbeom; V. Shapovalov, Maxim; Renfrew, P. Douglas; Mulligan, Vikram K.; Kappel, Kalli; Labonte, Jason W.; Pacella, Michael S.; Bonneau, Richard; Bradley, Philip; Dunbrack, Roland L.; Das, Rhiju; Baker, David; Kuhlman, Brian; Kortemme, Tanja; Gray, Jeffrey J.
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errSave
Accurate positioning of functional residues with robotics-inspired computational protein design
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2022-03-07
err8
errOAAI
errKrivacic, Cody; Kundert, Kale; Pan, Xingjie; Pache, Roland A.; Liu, Lin; Conchuir, Shane O.; Jeliazkov, Jeliazko R.; Gray, Jeffrey J.; Thompson, Michael C.; Fraser, James S.; Kortemme, Tanja
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errSave
Antibody structure prediction using interpretable deep learning
errPATTERNS
IF7.4
err2022-02-01
err105
errOAAI
errRuffolo, Jeffrey A.; Sulam, Jeremias; Gray, Jeffrey J.
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errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
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Zhiping Weng
H-index: 119 · Papers: 537
J
Jamie Rossjohn
H-index: 118 · Papers: 983
L
Luigi Cavallo
H-index: 112 · Papers: 1.2K
W
Wayne W. Hancock
H-index: 104 · Papers: 609
M
Michael J. Kuhar
H-index: 102 · Papers: 1.2K
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