GrayLab Publications | Johns Hopkins University

Preprints (not yet peer-reviewed)
1. Samanta R, Harmalkar A, Prathima P, Gray JJ "Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta,"bioRxiv (2024) Online.
2. Harmalkar A, Lyskov S, Gray JJ "Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange,"eLife (2024) Online.
3. Chungyoun M, Ruffolo JA, Gray JJ "FLAb: Benchmarking deep learning methods for antibody fitness prediction,"bioRxiv (2023) Online.
4. Harmalkar R, Lyskov S, Gray JJ "Reliable protein-protein docking with AlphaFold, Rosetta and replica-exchange,"eLife (2023) Online.
5. Mahajan SP, Ruffolo JA, Gray JJ "Contextual protein encodings from equivariant graph transformers,"bioRxiv (2023) Online.
6. Ruffolo JA, Gray JJ, Sulam J "Deciphering antibody affinity maturation with language models and weakly supervised learning,"bioRxiv (2021) Online.
2024
1. Martins M, dos Santos AM, da Costa CHS, Canner SW, Chungyoun M, Gray JJ, Skaf MS, Ostermeier M, Goldbeck R "Thermostability Enhancement of GH 62 a-l-Arabinofuranosidase by Directed Evolution and Rational Design," ACS Journal of Agricultural and Food Chemistry (2024) Online.
2. Samanta R, Gray JJ "Implicit model to capture electrostatic features of membrane environment," PLOS Computational Biology (2024) Online.
3. Hutchinson M, Ruffolo JA, Haskins N, Iannotti M, Vozza G, Pham T, Mehzabeen N, Shandilya H, Rickert K, Croasdale-Wood R, Damschroder M, Fu Y, Dippel A, Gray JJ, Kaplan G "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen," mAbs 16(1) (2024) Online.
4. Adolf-Bryfogle J, Labonte JW, Kraft JC, Shapovalov M, Raemisch S, Lütteke T, DiMaio F, Bahl CD, Pallesen J, King NP, Gray JJ, Kulp DW, Schief WR "Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design," PLOS Computational Biology 20(6):e1011895–e1011895 (2024) Online.
2023
1. Chu LC, Ruffolo J, Harmalkar A, Gray JJ "Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer," Protein Science 33(2) (2023) Online.
2. Shuai RW, Ruffolo JA, Gray JJ "IgLM: Infilling language modeling for antibody sequence design," Cell Systems 14(11):979-989.e4 (2023) Online.
3. Lensink M, Brysbaert G, Raouraoua N, et al. "Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment," Proteins 91(12):1658-1683 (2023) Online.
4. Chungyoun, M & Gray, JJ "AI Models for Protein Design are Driving Antibody Engineering," Current Opinion in Biomedical Engineering 28:100473 (2023) Online.
5. Ruffolo JA, Chu LS, Mahajan SP, Gray JJ "Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies ," Nature Communications 14:2389 (2023) Online.
6. Canner SW, Shanker S, Gray JJ "Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level," Frontiers in Bioinformatics 3 (2023) Online.
7. Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL Jr, Gray JJ, Sauna ZE "Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus.," Heliyon 9(4):e15032 (2023) Online.
8. Harmalkar A, Rao R, Honer J, Deisting W, Anlahr J, Hoenig A, Czwikla J, Sienz-Widmann E, Rau D, Rice A, Riley TP, Li D, Catterall HB, Tinberg CE, Gray JJ, Wei KY "Towards generalizable prediction of antibody thermostability using machine learning on sequence and structure features ," mAbs 15(1) (2023) Online.
9. Hess RA, Erickson OA, Cole RB, Isaacs JM, Alvarez-Clare S, Arnold J, Augustus-Wallace A, Ayoob JC, Berkowitz A, Branchaw J, Burgio KR, Cannon CH, Ceballos RM, Cohen CS, Coller H, Disney J, Doze VA, Eggers MJ, Ferguson EL, Gray JJ, Greenberg JT, Hoffmann A, Jensen-Ryan D, Kao RM, Keene AC, Kowalko JE, Lopez SA, Mathis C, Minkara M, Murren CJ, Ondrechen MJ, Ordoñez P, Osano A, Padilla-Crespo E, Palchoudhury S, Qin H, Ramírez-Lugo J, Reithel J, Shaw CA, Smith A, Smith RJ, Tsien F, Dolan EL "Virtually the same? Evaluating the effectiveness of remote undergraduate research experiences ," CBE-LSE 22(2) (2023) Online.
2022
1. Akpinaroglu D, Ruffolo JA, Mahajan SP, Gray JJ "Simultaneous prediction of antibody backbone and side-chain conformations with deep learning," PLOS One 17(6):e0258173 (2022) Online.
2. Mahajan SP, Ruffolo JA, Frick R, Gray JJ "Hallucinating structure-conditioned antibody libraries for target-specific binders," Frontiers in Immunology 13(Oct 2022):999034 (2022) Online.
3. Boorla VS, Chowdhury R, Ramasubramanian R, Ameglio B, Frick R, Gray JJ, Maranas CD "De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-Cov-2 spike receptor binding domains (RBO)," Proteins Structure, Function and Bioinformatics 91(2 ):196-208 (2022) Online.
4. Li Y, Cao B. Modali S, Lee E, Xu H, Petrenko V, Gray JJ, Yang M, Mao C "Understanding the interactions between bone mineral crystals and their binding peptides derived from filamentous phage," Materials Today Advances 15(1):100263 (2022) Online.
5. Harmalkar A, Mahajan SP, Gray JJ "Induced fit with replica exchange improves protein complex structure prediction," PLOS Comp. Bio. 18:1-21 (2022) Online.
6. Krivacic C, Kundert K, Pan X, Pache RA, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, Kortemme T "Accurate positioning of functional residues with robotics-inspired computational protein design," Proc. Natl. Acad. Sci. USA 119(11):e2115480119 (2022) Online.
7. Erickson OA, Cole RB, Isaacs JM, Alvarez-Clare S, Arnold, Augustus-Wallace A, Ayoob JC, Berkowitz A, Branchaw J, Burgio KR, Cannon CH, Ceballos RM, Cohen CS, Coller H, Disney J, Doze VA, Eggers MJ, Farina S, Ferguson EL, Gray JJ, Greenberg JT, Hoffmann A, Jensen-Ryan D, Kao RM, Keene AC, Kowalko JE, Lopez SA, Mathis C, Minkara M, Murren CJ, Ondrechen MJ, Ordonez P, Osano A, Padilla-Crespo E, Palchoudhury S, Qin H, Ramirez-Lugo J, Reithel J, Shaw CA, Smith A, Smith R, Summers AP, Tsien F, Dolan EL "“How do we do this at a distance?!” A descriptive study of remote undergraduate research programs during COVID-19," CBE—Life Sciences Education 21(1):1-16 (2022) Online.
8. Ruffolo J, Sulam J, Gray JJ "Antibody structure prediction using interpretable deep learning," Patterns 3(2):100406 (2022) Online.
9. Frick R, Høydahl LS, Hodnebrug I, Vik ES, Dalhus B, Sollid LM, Gray JJ, Sandlie I, Løset, GA "Affinity maturation of TCR-like antibodies using phage display guided by structural modeling," Protein Engineering Design and Selection 35(1) (2022) Online.
2021
1. Dempsey DR, Viennet T, Iwase R, Park E, Henriquez S, Chen Z, Jeliazkov JR, Palanski BA, Phan KL, Coote P, Gray JJ, Eck MJ, Gabelli SB, Arthanari H, Cole PA "The structural basis of PTEN regulation by multi-site phosphorylation," Nature Structural & Molecular Biology 28:858-868 (2021) Online.
2. Frick R, Hoydahl L, Petersen J, Du Pre, M, Kumari S, Bernsten G, Dewan A, Jeliazkov J., Gunnarsen K.,Frigstad T., Llerena C, Lundin K, Yaqub S, Jahnsen J, Gray JJ, Rossjohn J, Sollid L, Sandlie I, Loset G, "A high-affinity human TCR-like antibody detects celiac disease gluten peptide–MHC complexes and inhibits T cell activation," Science Immunology 6(62):4925 (2021) Online.
3. Cohen-Khait R, Harmalkar A, Pham P, Webby M, Housden N, Elliston E, Hopper J, Mohammed S, Robinson C, Gray JJ , Kleanthous C "Colicin-Mediated Transport of DNA through the Iron Transporter FepA," mBio 12(5):e01787-21 (2021) Online.
4. Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A "Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment," Proteins 89(12):1800-1823 (2021) Online.
5. Nance ML, Labonte JW, Adolf-Bryfogle J, Gray JJ. "Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta ," J. Phys. Chem. B 125(5):6807-6820 (2021) Online.
6. Leman JK, Lyskov S, Lewis S, Adolf-Bryfogle J, Alford R, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Lefeaver-Fay A, Gront D, Gray JJ, Bonneau R "Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks," Nature Communications 12(6947) (2021) Online.
7. Li M, Zheng X,Shanker S, Jaroentomeechai T, Moeller T, Hulbert S, Kocer I, Byrne J, Cox E, Fu Q, Zhang S, Labonte JW, DeLisa MP, Gray JJ "Shotgun scanning glycomutagenesis: A simple and efficient strategy for constructing and characterizing neoglycoproteins," Proc. Natl. Acad. Sci. USA 118(39):e2107440118 (2021) Online.
8. Alford RF, Samanta R, Gray JJ "Diverse scientific benchmarks for implicit membrane energy functions," J. Chem. Theor. Comput. 17(8):5248-5261 (2021) Online.
9. Le K, Adolf-Bryfogle J, Klima J, Lyskov S, Labonte J, Bertolani S, Roy Burman S, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz M, Alford R, Aleexan A, Nance M, Das R, Dunbrack R, Schief W, Kuhlman B, Siegel J, Gray JJ "PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design ," The Biophysicist 2(1):108-122 (2021) Online.
10. Jeliazkov JR, Frick R, Zhou J, Gray JJ "Robustification of RosettaAntibody and Rosetta SnugDock," PLoS ONE 16(3):e0234282 (2021) Online.
11. Harmalkar A, Gray JJ "Advances to tackle backbone flexibility in protein docking," Current Opinion in Structural Biology 67:178-186 (2021) Online.
12. Mahajan SP, Srinivasan Y, Labonte JW, DeLisa MP, Gray JJ "Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2," ACS Catalysis 11 (5):2977–2991 (2021) Online.
13. Guest JD ,Vreven T, Zhou J, Moal I, Jeliazkov J, Gray JJ, Weng Z, Pierce BG "An Expanded Benchmark for Antibody-Antigen Docking and Affinity Prediction Reveals Insights into Antibody Recognition Determinants," Structure 29(2):606-621 (2021) Online.
14. Vater A, Mayoral J, Nunez-Castilla J, Labonte JW, Briggs LA, Gray JJ, Makarevitch I, Rumjahn SM, Siegel JB "Development of a Broadly Accessible, Computationally Guided Biochemistry Course-Based Undergraduate Research Experience," J. Chem. Ed. 98(2):400-409 (2021) Online.
2020
1. Gao W, Mahajan SP, Sulam J, & Gray, JJ "Deep Learning in Protein Structural Modeling and Design," Patterns 1(9):100142 (2020) Online.
2. Alford RF, Smolin N, Young HS, Gray JJ, Robia SL "Protein Docking and Steered Molecular Dynamics Suggest Alternative Phospholamban-binding Sites on the SERCA Calcium Transporter," Journal of Biological Chemistry 295(32):11262-11274 (2020) Online.
3. Ruffolo JA, Guerra C, Mahajan SP, Sulam J, Gray JJ "Geometric Potentials from Deep Learning Improve Prediction of CDR H3 Loop Structures," Bioinformatics 36(Supplement_1):i268-i275 (2020) Online.
4. Leman, JK, Weitzner, BD, Lewis, SM, Alford RF,Gray JJ, Burman, R, Labonte, JW, Jeliazkov JR, Marze NA, Lubin JH, Lyskov S, Bonneau R, et al "Macromolecular modeling and design in Rosetta: recent methods and frameworks.," Nature Methods 17:665-680 (2020) Online.
5. Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, et al. "Better together: Elements of successful scientific software development in a distributed collaborative community," PLoS Comput Biol 16(5):e1007507 (2020) Online.
6. Alford RF, Fleming PJ, Fleming KG, Gray JJ "Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane ," Biophysical Journal 118(8):2024-2055 (2020) Online.
2019
1. Roy Burman SS, Nance ML, Jeliazkov J, Labonte JW, Lubin JH, Biswas N, Gray JJ "Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI Rounds 37–45," Proteins 88(8):973-985 (2019) Online.
2. Lee J, Der BS, Karamitros CS, Li W, Marshall NM, Lungu OI, Miklos AE, Xu J, Kang TH, Lee C Tan B, Hughes RA, Jung ST, Ippolito GC, GrayJJ, Zhang Y, Kuhlman B, Georgiou G, Ellington AD "Computer-based engineering of thermostabilized antibody fragments," AICHE Journal 66(3):e16864 (2019) Online.
3. Jeliazkov JR, Robinson AC, García-Moreno BE, Berger JM, Gray JJ "Toward computational design of protein crystals with improved resolution," Acta Crystallographica Section D D75:1015-1027 (2019) Online.
4. Fernandez AJ, Earnest JPD, Mahajan SP, Gray JJ, Gerken AT, Tabak LA, Samara N L "The structure of the colorectal cancer associated enzyme GalNAc-T12 reveals how non-conserved residues dictate its function," Proc. Natl. Acad. Sci. USA 116:20404-20410 (2019) Online.
5. Santiago-Frangos A, Frohlich KS, Jeliazkov JR, Malecka EM, Marino G, Gray JJ, Luisi BF, Woodson SA, Hardwick SW "Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation," Proc. Natl. Acad. Sci. USA 116(22):10978-10987 (2019) Online.
6. Høydahl LS, Richter L, Snir O, Frick R, Gunnarsen KS, Landsverk OJB, Iversen R, Fleur du Pre M, Jeliazkov JR, Gray JJ, Bergseng E, Foss S, Qiao S-W, Lundin KEA, Jahnsen J, Sandlie I, Sollid LM & Løset GÅ, "Plasma Cells Are the Most Abundant Gluten Peptide MHC-expressing Cells in Inflamed Intestinal Tissues From Patients With Celiac Disease," Gastroenterology 156(5):1428-1439.e10 (2019) Online.
7. Roy Burman SS, Yovanno RA, Gray JJ "Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes," Structure 27(6):1041-1051.e8 (2019) Online.
8. Long X, Jeliazkvo J, Gray JJ "Non-H3 CDR template selection in antibody modeling through machine learning," PeerJ 7(e6179) (2019) Online.
9. Spear, ED, Alford RF, Babatz T, Wood K, Mossberg O, Odinammadu K, Shilgardi K, Gray JJ & Michaelis S "A Humanized Yeast System to Analyze Cleavage of Prelamin A by ZMPSTE24," Methods 157:47-55 (2019) Online.
2018
1. Chien Y-C, Mansouri A, Jiang W, Khan SR, Gray JJ, McKee MD, "Modulation of calcium oxalate dihydrate growth by phosphorylated osteopontin peptides," Journal of Structural Biology 204(2):131-144 (2018) Online.
2. Jiang W, Pacella MS, Vali H, Gray JJ, McKee MD, "Chiral Switching in Biomineral Suprastructures Induced by Homochiral L-Amino Acid," Science Advances 4(8) (2018) Online.
3. Moretti R, Lyskov S, Das R, Meiler J, Gray JJ, "Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)," Protein Science 27(1):259-268 (2018) Online.
4. Lubin JH, Pacella MS & Gray JJ "A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces," Langmuir 34(18):5279-5289 (2018) Online.
5. Kalin J, Wu M, Gomez A, Song Y, Das J, Hayward D, Adejola N, Wu M, Panova I, Hy Chung H J, Kim E, Roberts H, Roberts J, Prusevich P, Jeliazkov J, Roy Burman S, Fairall L, Milano C, Eroglu A, Proby C, Dinkova-Kostova A, Hancock W, Gray J, Bradner J, Valente S, Mai A, Anders N, Rudek M, Hu Y, Ryu B, Schwabe J, Mattevi A, Alani R & Cole P "Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors," Nature Communications 9:53 (2018) Online.
6. Athanasiadou D, Jiang W, Goldbaum D, Saleem A, Basu K, Pacella M, Böhm C, Chromik R, Hincke M, Rodríguez-Navarro A, Vali H, Wolf S, Gray JJ, Bui K & McKee M, "Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell," Science Advances 4(3):eaar3219 (2018) Online.
7. Pacella MS & Gray JJ "A Benchmarking Study of Peptide-Biomineral Interactions," Crystal Growth and Design 18(2):607-616 (2018) Online.
8. Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Tsumoto K & Gray JJ "Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification," Frontiers in Immunology 9(413) (2018) Online.
9. Marze NA, Roy Burman SS, Sheffler W & Gray JJ "Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets," Bioinformatics 34(20):3461-3469 (2018) Online.
10. Koehler Leman J, Mueller BK & Gray JJ "Expanding the toolkit for membrane protein modeling in Rosetta," Bioinformatics 33(5):754-756 (2018) Online.
2017
1. Alford RF, Leaver-Fay A, Gonzales L, Dolan EL, Gray JJ "A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design," PLoS Computational Biology 13(2):e1005837 (2017) Online.
2. Koehler Leman J, D'Avino AR, Bhatnagar Y, Gray JJ "Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality," Proteins 86(1):57-74 (2017) Online.
3. Kilambi KP, Gray JJ "Structure-based cross-docking analysis of antibody–antigen interactions," Scientific Reports 7:8145 (2017) Online.
4. Santiago-Frangos A, Jeliazkov JR, Gray JJ, Woodson SA "Acidic C-terminal domains autoregulate the RNA chaperone Hfq," eLife 6:e27049 (2017) Online.
5. Mathew M, Tan E, Labonte JW, Shah S, Saeui CT, Liu L, Bhattacharya R, Bovonratwet P, Gray JJ & Yarema K, "Glycoengineering of esterase activity through metabolic flux-based modulation of sialic acid.," ChemBioChem 18(13):1204-1215 (2017) Online (*Equal contribution authors).
6. Newman A, Meluh P, Lu J, Vidal J, Carson C, Lagesse E, Gray JJ, Boeke J, Matunis M. "A high throughput mutagenic analysis of yeast sumo structure and function.," PLoS Genet 13(2):e1006612 (2017) Online.
7. Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FD, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, Das R, Baker D, Kuhlman B, Kortemme T & Gray JJ "The Rosetta all-atom energy function for macromolecular modeling and design," J. Chem. Theor. Comput. 13(6):3031-3048 (2017) Online.
8. Jiang W, Pacella MS, Athansiadou D, Nelea V, Vali H, Hazen RM, Gray JJ, & McKee MD "Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate," Nature Communications 8:15066 (2017) Online.
9. Labonte JW, Adolf-Bryfogle J, Schief WR, & Gray JJ "Residue-Centric Modeling and Design of Saccharide and Glycoconjugate Structures," J. Comput. Chem. 38(5):276-287 (2017) Online.
10. Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle A, Biswas N & Gray JJ "Modeling and docking antibody structures with Rosetta," Nature Protocols 12(2):401-416 (2017) Online.
11. Weitzner BD & Gray JJ "Accurate structure prediction of CDR H3 loops enabled by a novel structure-based C-terminal constraint," J. Immunology 198(1):505-515 (2017) Online.
12. Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE, DiMaio F & Gray JJ "Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35," Proteins 85(3):479-486 (2017) Online.
2016
1. Marze NA, & Gray JJ. "Improved Prediction of Antibody VL-VH Orientation," Protein Eng. Des. Sel. 29(10):409-418 (2016) Online.
2. Piepenbrik KH, Lillehoj E, Harding CM, Labonte JW, Zuo X, Rapp CA, Munson RS, Goldblum SE, Feldman MF, Gray JJ & Sundberg EJ "Structural diversity in the type IV pili of multidrug-resistant Acinetobacter," J. Biol. Chem. 291:22924-22935 (2016) Online.
3. Kuroda, D & Gray, JJ. "Pushing the Backbone in Protein-Protein Docking," Structure 24(10):1821-1829 (2016) Online.
4. Lensink M, Velankar S, Kryshtafovych A, Huang S, Duhovny-Schneidman D, Sali A, Marze N, Roy Burman S, Kuroda D, Gray JJ, Wodak S [82 authors total] "Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment," Proteins 84(51):323-348 (2016).
5. Kuroda, D & Gray, JJ "Shape complementarity of hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking," Bioinformatics 32(16):2451-2456 (2016) Online.
6. DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D, Ellington AD, Ippolito GC, Gray JJ, & Georgiou G. "Large-Scale Sequence and Structural Comparisons of Human Naive and Antigen-Experienced Antibody Repertoires," Proc. Natl. Acad. Sci. USA 113(19):E2636-45 (2016) Online (^*these authors contriubted equally to this work).
2015
1. Alford RF, Koehler Leman J, Weitzner BD, Duran AM, Tilley DC, Elazar A & Gray JJ. "An integrated framework advancing membrane protein modeling and design," PLoS Comput. Biol. 11(9):e1004398 (2015) Online.
2. Pierre B, Labonte JW, Xiong T, Aoraha E, Williams A, Shah V, Chau E, Helal KY, Gray JJ & Kim JR. "Molecular determinants for protein stabilization by insertional fusion to a thermophilic host protein," ChemBioChem 16(16):2392-2402 (2015) Online.
3. Matlahov I, Iline-Vul T, Abayev M, Lee Y, Nadav-Tsubery M, Keinan-Adamsky K, Gray JJ & Goobes G "Interfacial mineral-peptide properties of a mineral binding peptide from osteonectin and bone-like apatite," Chem. Mater. 27(16):5562-5569 (2015) Online.
4. Jiang Q, Arnold S, Heanue T, Kilambi KP, Doan B, Kapoor A, Ling AY, Sosa MX, Guy M, Jiang Q, Burzynski G, West K, Bessling S, Griseri P, Amiel J, Fernandez RM, Verheij JBGM, Hofstra RMW, Borrego S, Lyonnet S, Ceccherini I, Gray JJ, Pachnis V, McCallion AS & Chakravarti A. "Functional Loss of Semaphorin 3C and/or Semaphorin 3D and Their Epistatic Interaction with Ret Are Critical to Hirschsprung Disease Liability," Am. J. Human Genetics 96(4):581-596 (2015) Online.
5. Weitzner BD, Dunbrack R & Gray JJ. "The origin of CDR H3 structural diversity," Structure 23(2):302-311 (2015) Online.
6. Koehler Leman J, Ulmschneider MB & Gray JJ. "Computational Modeling of Membrane Proteins," Proteins 83(1):1-24 (2015) Online.
2014
1. Kilambi KP, Reddy K, Gray JJ "Protein-protein docking with dynamic residue protonation states," PLoS Computational Biology 10(12):e1004018 (2014) Online.
2. Weitzner B, Kuroda D, Marze N, Xu J, Gray JJ "Blind Prediction Performance of RosettaAntibody 3.0: Grafting, Relaxation, Kinematic Loop Modeling, and CDR Optimization," Proteins 82(8):1611-1623 (2014) Online (^*these authors contriubted equally to this work).
3. Firnberg E, Labonte JW, Gray JJ, Ostermeier M "A Comprehensive, High-Resolution Map of a Gene's Fitness Landscape," Mol. Biol. Evol. 31(6):1581-1592 (2014) Online.
4. Xu J, Tack D, Hughes RA, Ellington AD, Gray JJ "Structure-based Non-canonical Amino Acid Design to Covalently Crosslink an Antibody-Antigen Complex," J. Struct. Biol. 185(2):215-222 (2014) Online.
5. Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond ASJ, Karaca E, Schmitz C, van Dijk M, Bonvin AMJJ, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Kilambi KP, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou H-X, Huang, S-Y, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ "Blind Prediction of Interfacial Water Positions in CAPRI," Proteins 82(4):620-632 (2014) Online.
2013
1. Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter J, Muthu P, Drew K, Kuroda D , Schueler-Furman O, Bonneau R, Gray JJ "Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27," Proteins 81(12):2201-2209 (2013) Online.
2. Pacella MS, Koo DCE, Thottungal RA, Gray JJ "Using the RosettaSurface Algorithm to Predict Protein Structure at Mineral Surfaces," Meth. Enz. 532:343-366 (2013) Online.
3. Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Pacella M, Kilambi KP, Gray JJ, Velankar S, Janin J, Wodak, S. J, Baker D (about 70 total authors) "Community-wide Evaluation of Methods for Predicting the Effect of Mutations on Protein-Protein Interactions," Proteins 81(11):1980-1987 (2013) Online.
4. Drew K, Renfrew PD, Craven T, Butterfoss GL, Chou F-C, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, Kirshenbaum K, Arora PS, Das R, Bonneau R. "Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design," PLoS One 8(7):e67051 (2013) Online.
5. DeR DS, Kluwe C, Miklos AE, Jacak R, Lyskov S, Gray JJ, Georgiou G, Ellington AD, Kuhlman B. "Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability," PLoS One 8(5):e64363 (2013) Online.
6. Lyskov S, Chou F-C, Conchúir S Ó, Der, B S, Drew K, Kuroda D, Xu J, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R "Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)," PLoS One 8(5):e63906 (2013) Online (^*these authors contriubted equally to this work; ^†;co-corresponding authors).
7. Leaver-Fay A, O'Meara MJ, Tyka M, Jacak, R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, Baker D, Kuhlman B. "Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement," Meth. Enz. 523:109-143 (2013) Online.
8. Tarasevich B, Perez-Salas U, Masica DL, Philo J, Kienzle P, Srueger S, Majkrzak, CF, Gray JJ, Shaw WJ "Neutron Reflectometry Studies of the Adsorbed Structure of the Amelogenin, LRAP," J. Phys. Chem. B 117(11):3098-3109 (2013) Online.
2012
1. Chaikind B, Kilambi KP, Gray JJ, Ostermeier M "Targeted DNA Methylation Using an Artificially Bisected M.HhaI Fused to Zinc Fingers," PLoS One 7(9):e44852 (2012) Online.
2. Kilambi KP, Gray JJ "Rapid Calculation of Protein pKa Values using Rosetta," Biophys. J. 103(3):587-595 (2012) Online.
3. Ye Y, Stahley MR, Xu J, Friedman JI, Sun Y, McKnight JN, Gray JJ, Bowman GD, Stivers JT "Enzymatic Excision of Uracil Residues in Nucleosomes Depends on the Local DNA Structure and Dynamics," Biochemistry 51(30):6028-6038 (2012) Online.
4. Miklos AE, Kluwe C, Der BS, Pai S, Sircar A, Hughes RA, Berrondo M, Xu J, Codrea V, Buckley PE, Calm AM, Welsh HS, Warner CR, Zacharko MA, Carney JP, Gray JJ, Georgiou G, Kuhlman B, Ellington AD "Structure-Based Design of Supercharged, Highly Thermoresistant Antibodies," Chemistry & Biology 19(4):449-455 (2012) Online.
2011
1. Schrier SB, Sayeg MK, Gray JJ "Prediction of Calcite Morphology from Computational and Experimental Studies of Mutations of a De Novo Designed Peptide," Langmuir 27(18):11520-11527 (2011) Online.
2. Fleishman SJ, Whitehead TA, Strauch EMand about 95 others including Kilambi KP, Sircar A, and Gray JJ "Community-wide assessment of protein-interface modeling suggests improvements to design methodology," J. Mol. Biol. 414(2):289-302 (2011) Online.
3. Chaudhury S, Berrondo M, Weitzner BD, Muthu P, Bergman H, Gray JJ "Benchmarking and analysis of protein docking performance in RosettaDock 3.2," PLoS One 6(8):e22477 (2011) Online.
4. Baugh E, Lyskov S, Weitzner BD, Gray JJ "Real-time PyMOL visualization for Rosetta and PyRosetta," PLoS One 6(8):e21931 (2011) Online.
5. Berrondo M, Gray JJ "Computed structures of point deletion mutants and their enzymatic activities," Proteins 79(10):2844-2860 (2011) Online (Featured Cover Art).
6. Masica DL, Gray JJ, W. Shaw W "Partial high-resolution structure of phosphorylated and non-phosphorylated leucine-rich amelogenin protein adsorbed to hydroxyapatite," J. Phys. Chem. C 115(28):13775-13785 (2011) Online (^†co-corresponding authors).
7. Sircar A, Sanni KA,Shi J, Gray JJ "Analysis and Modeling of the Variable Region of Camelid Single Domain Antibodies," J. Immunology 186(11):6357-6367 (2011) Online | Supplementary Material.
8. McKee MD, Nakano Y, Masica DL, Gray JJ, Lemire I, Heft R, Crine P, Millan JL "Enzyme Replacement Therapy Prevents Dental Defects in a Model of Hypophosphatasia," J. Dental Res. 90(4):470-476 (2011) Online (Featured Cover Art).
9. Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Fichter F, Ban Y-EA, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popovic Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, D Baker D, Bradley P "Rosetta3: An object-oriented software suite for the simulation and design of macromolecules," Meth. Enz. 487:545-574 (2011) Online.
10. Bocik WE, Sircar A, Gray JJ, Tolman JR "Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2," J. Biol. Chem. 286(5):3981-3991 (2011) Online (^†co-corresponding authors).
2010
1. Masica DL, Ashworth J, Ndao M, Drobny G, Gray JJ "Toward a structure determination method for biomineral-associated protein using combined solid-state NMR and computational structure prediction," Structure 18(12):1678-1687 (2010) Online.
2. Keshet B, Gray JJ, Good TA "Structurally distinct toxicity inhibitors bind at common loci on beta-amyloid fibril," Prot. Sci. 19(12):2291-2304 (2010) Online.
3. Masica DL, Schrier SB, Specht E, Gray JJ "De novo design of peptide-calcite biomineralization systems," J. Am. Chem. Soc. 132(35):12252-12262 (2010) Online.
4. Sircar A, Chaudhury S, Kilambi KP, Berrondo M, Gray JJ "A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19," Proteins 78(15):3115-3123 (2010) Online.
5. Berrondo M, Gray JJ, Schleif R "Computational predictions of the mutant behavior of AraC," J. Mol. Biol. 398(3):462-470 (2010) Online.
6. Chaudhury S, Lyskov S, Gray JJ "PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta," Bioinformatics 26(5):689-691 (2010) Online.
7. Sircar A, Gray JJ "SnugDock: Paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models," PLoS Comput. Biol. 6(1):e1000644 (2010) Online.
8. Addison WN, Masica DL, Gray JJ, McKee MD "Phosphorylation-dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage," J. Bone & Mineral Research 25(4):695-705 (2010) Online.
2009
1. Chaudhury S, Gray JJ "Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking and implications for drug resistance," Structure 17(12):1636-1648 (2009) Online.
2. Chien Y-C, Masica DL, Gray JJ, Nguyen S, Vali H, McKee MD "Modulation of calcium oxalate dehydrate growth by selective crystal-face binding of phosphorylated osteopontin and poly-aspartate peptide showing occlusion by sectoral (compositional) zoning," J. Biol. Chem. 284:23491-23501 (2009) Online.
3. Sircar A, Kim E, Gray JJ "RosettaAntibody: Antibody Variable Region Homology Modeling Server," Nucleic Acids Research 37(Web Server Issue):W474-W479 (2009) Online (^*these authors contriubted equally to this work).
4. Masica DL, Gray JJ "Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system," Biophys. J. 96(8):3082-3091 (2009) Online.
5. Daily MD, Gray JJ "Allosteric communication occurs via networks of tertiary and quaternary motions in proteins," PLoS Comput. Biol. 5(2):e1000293 (2009) Online.
6. Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ "Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking," Proteins 74(2):497-514 (2009) Online (^*these authors contriubted equally to this work).
2008
1. Chaudhury S, Gray JJ "Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles," J. Mol. Biol. 381(4):1068-1087 (2008) Online.
2. Lyskov S, Gray JJ "The RosettaDock server for local protein-protein docking," Nucleic Acids Research 36(Web Server Issue):W233-W238 (2008) Online.
3. Pickin K, Chaudhury S, Dancy B, Gray JJ, Cole P "Analysis of protein kinase autophosphorylation using expressed protein ligation and computational modeling," J. Am. Chem. Soc. 130(17):5667-5669 (2008) Online.
4. Berrondo M, Ostermeier M, Gray JJ "Structure prediction of domain insertion proteins from structures of the individual domains," Structure 16(4):513-527 (2008) Online.
5. Daily MD, Upadhyaya TJ, Gray JJ "Contact rearrangements form coupled networks from local motions in allosteric proteins," Proteins 71(1):455-466 (2008) Online | Supplementary Material.
6. Sivasubramanian A, Maynard JA, Gray JJ "Modeling the structure of mAb 14B7 bound to the anthrax protective antigen," Proteins 70(1):218-230 (2008) Online.
2007
1. Makrodimitris K, Masica DL, Kim ET, Gray JJ "Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite," J. Am. Chem. Soc. 129(44):13713-13722 (2007) Online.
2. Chaudhury S, Sircar A, Sivasubramanian A, Berrondo M, Gray JJ "Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12," Proteins 69(4):793-800 (2007) Online (^*these authors contriubted equally to this work).
3. Meitzler J, Gray JJ, Hendrickson TL "Truncation of the caspase-related subunit (Gpi8p) of Saccharomyces cerevisiae GPI transamidase: Dimerization revealed," Arch. Biochem. Biophys. 462(1):83-93 (2007) Online.
4. Daily MD, Gray JJ "Local motions in a benchmark of allosteric proteins," Proteins 67(2):385-399 (2007) Online | Supplementary Material.
2006
1. Gray JJ "Biomolecular Modeling in a Process Dynamics and Control Course," Chemical Engineering Education 40(4):297-306 (2006) Online.
2. Gray JJ "High-resolution protein-protein docking," Curr. Op. Struct. Biol. 16(2):183-193 (2006) Online.
3. Sivasubramanian A, Chao G, Pressler HM, K Witrup KD, Gray JJ "Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis," Structure 14(3):401-414 (2006) Online.
2005
1. Daily MD, Masica D, Sivasubramanian A, Somarouthu S, and Gray JJ "CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock," Proteins 60(2):181-186 (2005) Online.
2. Singh P, Mhaka AM, Christensen SB, Gray JJ, Denmeade SR, Isaacs JT "Applying linear interaction energy method for rational design of non-competitive allosteric inhibitors of the SERCA ATPase," J. Med. Chem. 48(8):3005-3014 (2005) Online.
2004
1. Gray JJ "The Interaction of Proteins with Solid Surfaces," Curr. Op. Struct. Biol. 14(1):110-115 (2004) Online.
2003
1. Gray JJ, Moughan SE, Kortemme T, Schueler-Furman O, Misura KMS, Morozov AV, Baker D "Protein-Protein Docking Predictions for the CAPRI Experiment," Proteins 52(1):118-122 (2003) Online.
2. Gray JJ, Moughan SE, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D "Protein-Protein Docking with Simultaneous Optimization of Rigid-Body Displacement and Side-Chain Conformations," J. Mol. Biol. 331(1):281-299 (2003) Online.
2001
1. Gray JJ, Klein DH, Korgel BA, Bonnecaze RT "Microstructure formation and kinetics in the random sequential adsorption of polydisperse tethered nanoparticles modeled as hard disks," Langmuir 17(8):2317-2328 (2001) Online.
2. Gray JJ, Bonnecaze RT "Adsorption of colloidal particles by Brownian dynamics simulation: kinetics and surface structures," J. Chem. Phys. 114(3):1366 (2001) Online.
3. Gray JJ, Bonnecaze RT "Adsorption of charge-bidisperse mixtures of colloidal particles," Langmuir 17(25):7935-7947 (2001) Online.
2000 & Older
1. Gray JJ, Klein DH, Bonnecaze RT, Korgel BA "Non-equilibrium phase behavior during the random sequential adsorption of tethered hard disks," Phys. Rev. Lett. 85(21):4430-4433 (2000) Online.
2. Gray JJ, Chiang B, Bonnecaze RT "Origin of anomalous multibody interactions," Nature 402:750 (1999) Online (brief communication).
3. Gray JJ, Bonnecaze RT "Rheology and dynamics of sheared arrays of colloidal particles," J. Rheology 42(5):1121-1151 (1998) Online.
4. Lee GM, Gray JJ, and Palsson BO "Effect of trisodium citrate treatment on hybridoma cell viability," Biotechnology Techniques 5(4):295-298 (1991).