Research output per year
Research output per year
- 1 - 50 out of 146 results
Search results
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2025
Queer voices in computational biology: the first ISCB LGBTQI+ Symposium
Parra, R. G., Wass, M. N., Munholland, S., Wiper, M. L., Kovats, D., Pantano, L. & Dunbrack, R. L., 2025, In: Bioinformatics Advances. 5, 1, p. vbae204 vbae204.Research output: Contribution to journal › Article › peer-review
Open Access -
2024
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
Critical Assessment of Genome Interpretation Consortium & Dunbrack, R., Jan 22 2024, In: Genome Biology. 25, 1, p. 53 53.Research output: Contribution to journal › Article › peer-review
Open Access13 Scopus citations -
E proteins control the development of NKγδT cells through their invariant T cell receptor
Mihai, A., Lee, S. Y., Shinton, S., Parker, M. I., Contreras, A. V., Zhang, B., Rhodes, M., Dunbrack, R. L., Zúñiga-Pflücker, J. C., Ciofani, M., Zhuang, Y. & Wiest, D. L., Dec 2024, In: Nature Communications. 15, 1, p. 5078 5078.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Exploring Co-occurring POLE Exonuclease and Non-exonuclease Domain Mutations and Their Impact on Tumor Mutagenicity
Shah, S. M., Demidova, E. V., Ringenbach, S., Faezov, B., Andrake, M., Gandhi, A., Mur, P., Viana-Errasti, J., Xiu, J., Swensen, J., Valle, L., Dunbrack, R. L., Hall, M. J. & Arora, S., Jan 26 2024, In: Cancer Res Commun. 4, 1, p. 213-225 13 p.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
FAM122A ensures cell cycle interphase progression and checkpoint control by inhibiting B55α/PP2A through helical motifs
Wasserman, J. S., Faezov, B., Patel, K. R., Kurimchak, A. M., Palacio, S. M., Glass, D. J., Fowle, H., McEwan, B. C., Xu, Q., Zhao, Z., Cressey, L., Johnson, N., Duncan, J. S., Kettenbach, A. N., Dunbrack, R. L. & Graña, X., Jul 10 2024, In: Nature Communications. 15, 1, p. 5776 5776.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Impact of primary sequence changes on the self-association properties of mammalian cystathionine beta-synthase enzymes
Lee, H., Gupta, K., Wang, L., Dunbrack, R. L., Majtan, T. & Kruger, W. D., Dec 2024, In: Protein Science. 33, 12, e5223.Research output: Contribution to journal › Article › peer-review
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PAK2 is necessary for myelination in the peripheral nervous system
Hu, B., Moiseev, D., Schena, I., Faezov, B., Dunbrack, R., Jonathan, C. & Li, J., May 1 2024, In: Brain. 147, 5, p. 1809-1821 13 p., awad413.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
2023
Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing
Demidova, E. V., Serebriiskii, I. G., Vlasenkova, R., Kelow, S., Andrake, M. D., Hartman, T. R., Kent, T., Virtucio, J., Rosen, G. L., Pomerantz, R. T., Dunbrack, R. L., Golemis, E. A., Hall, M. J., Chen, D. Y. T., Daly, M. B. & Arora, S., Mar 24 2023, In: Bmc Genomics. 24, 1, p. 212 212.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
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
Hernandez, N. E., Jankowski, W., Frick, R., Kelow, S. P., Lubin, J. H., Simhadri, V., Adolf-Bryfogle, J., Khare, S. D., Dunbrack, R. L., Gray, J. J. & Sauna, Z. E., Apr 2023, In: Heliyon. 9, 4, p. e15032 e15032.Research output: Contribution to journal › Article › peer-review
Open Access7 Scopus citations -
Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing
Demidova, E. V., Serebriiskii, I. G., Vlasenkova, R., Kelow, S., Andrake, M. D., Hartman, T. R., Kent, T., Virtucio, J., Rosen, G. L., Pomerantz, R. T., Dunbrack, R. L., Golemis, E. A., Hall, M. J., Chen, D. Y. T., Daly, M. B. & Arora, S., Jun 10 2023, In: BMC Genomics. 24, 1, p. 388 388.Research output: Contribution to journal › Article › peer-review
Open Access -
Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study
Schweke, H., Xu, Q., Tauriello, G., Pantolini, L., Schwede, T., Cazals, F., Lhéritier, A., Fernandez-Recio, J., Rodríguez-Lumbreras, L. A., Schueler-Furman, O., Varga, J. K., Jiménez-García, B., Réau, M. F., Bonvin, A. M. J. J., Savojardo, C., Martelli, P. L., Casadio, R., Tubiana, J., Wolfson, H. J. & Oliva, R. & 26 others, , Sep 2023, In: Proteomics. 23, 17, p. e2200323 2200323.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth
Tang, R., Shuldiner, E. G., Kelly, M., Murray, C. W., Hebert, J. D., Andrejka, L., Tsai, M. K., Hughes, N. W., Parker, M. I., Cai, H., Li, Y. C., Wahl, G. M., Dunbrack, R. L., Jackson, P. K., Petrov, D. A. & Winslow, M. M., Jan 2023, In: Nature Cell Biology. 25, 1, p. 159-169 11 p.Research output: Contribution to journal › Article › peer-review
Open Access13 Scopus citations -
Palmitoylation-dependent control of JAK1 kinase signaling governs responses to neuropoietic cytokines and survival in DRG neurons
Hernandez, L. M., Montersino, A., Niu, J., Guo, S., Faezov, B., Sanders, S. S., Dunbrack, R. L. & Thomas, G. M., Aug 2023, In: Journal of Biological Chemistry. 299, 8, p. 104965 104965.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
The protein common assembly database (ProtCAD)––a comprehensive structural resource of protein complexes
Xu, Q. & Dunbrack, R. L., Jan 6 2023, In: Nucleic Acids Research. 51, D1, p. D466-D478Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
2022
Delineating the RAS Conformational Landscape
Parker, M. I., Meyer, J. E., Golemis, E. A. & Dunbrack, R. L., Jul 1 2022, In: Cancer Research. 82, 13, p. 2485-2498 14 p.Research output: Contribution to journal › Article › peer-review
Open Access18 Scopus citations -
Development and Utility of a PAK1-Selective Degrader
Chow, H. Y., Karchugina, S., Groendyke, B. J., Toenjes, S., Hatcher, J., Donovan, K. A., Fischer, E. S., Abalakov, G., Faezov, B., Dunbrack, R., Gray, N. S. & Chernoff, J., Nov 8 2022, In: Journal of Medicinal Chemistry. 65, 23, p. 15627-15641 15 p.Research output: Contribution to journal › Article › peer-review
Open Access11 Scopus citations -
Investigation of the causal etiology in a patient with T-B+NK+ immunodeficiency
Sertori, R., Lin, J. X., Martinez, E., Rana, S., Sharo, A., Kazemian, M., Sunderam, U., Andrake, M., Shinton, S., Truong, B., Dunbrack, R. M., Liu, C., Srinivasan, R., Brenner, S. E., Seroogy, C. M., Puck, J. M., Leonard, W. J. & Wiest, D. L., Jul 29 2022, In: Frontiers in Immunology. 13, p. 928252 928252.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Kincore: A web resource for structural classification of protein kinases and their inhibitors
Modi, V. & Dunbrack, R. L., Jan 7 2022, In: Nucleic Acids Research. 50, D1, p. D654-D664Research output: Contribution to journal › Article › peer-review
Open Access52 Scopus citations -
PDBe-KB: collaboratively defining the biological context of structural data
PDBe-KB consortium, 2022, In: Nucleic Acids Research. 50, D1, p. D534-D542Research output: Contribution to journal › Article › peer-review
Open Access58 Scopus citations -
The ERK2-DBP domain opposes pathogenesis of a mouse JAK2V617F-driven myeloproliferative neoplasm
Zhang, Y., Truong, B., Fahl, S. P., Martinez, E., Cai, K. Q., Al-Saleem, E. D., Gong, Y., Liebermann, D. A., Soboloff, J., Dunbrack, R., Levine, R. L., Fletcher, S., Kappes, D., Sykes, S. M., Shapiro, P. & Wiest, D. L., Jul 28 2022, In: Blood. 140, 4, p. 359-373 15 p.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
2021
PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences
Faezov, B. & Dunbrack, R. L., Jul 2021, In: PLoS ONE. 16, 7 July, p. e0253411 e0253411.Research output: Contribution to journal › Article › peer-review
Open Access22 Scopus citations -
PP2A/B55α substrate recruitment as defined by the retinoblastoma-related protein p107
Fowle, H., Zhao, Z., Xu, Q., Wasserman, J. S., Wang, X., Adeyemi, M., Feiser, F., Kurimchak, A., Atar, D., McEwan, B. C., Kettenbach, A. N., Page, R., Peti, W., Dunbrack, R. L. & Grana, X., Oct 2021, In: eLife. 10, e63181.Research output: Contribution to journal › Article › peer-review
Open Access22 Scopus citations -
Structure of TFIIK for phosphorylation of CTD of RNA polymerase II
van Eeuwen, T., Li, T., Kim, H. J., Gorbea Colón, J. J., Parker, M. I., Dunbrack, R. L., Garcia, B. A., Tsai, K. L. & Murakami, K., Apr 7 2021, In: Science advances. 7, 15, eabd4420.Research output: Contribution to journal › Article › peer-review
Open Access10 Scopus citations -
2020
Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody DE loop for antibody-antigen binding
Dunbrack, R. L., Jan 1 2020, In: mAbs. 12, 1, 1840005.Research output: Contribution to journal › Article › peer-review
Open Access23 Scopus citations -
Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction
Shapovalov, M., Dunbrack, R. L. & Vucetic, S., May 2020, In: PLoS ONE. 15, 5, e0232528.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
ProtCID: a data resource for structural information on protein interactions
Xu, Q. & Dunbrack, R. L., Dec 1 2020, In: Nature Communications. 11, 1, 711.Research output: Contribution to journal › Article › peer-review
Open Access42 Scopus citations -
2019
A new clustering and nomenclature for beta turns derived from high-resolution protein structures
Shapovalov, M., Vucetic, S. & Dunbrack, R. L., Mar 2019, In: PLoS Computational Biology. 15, 3, e1006844.Research output: Contribution to journal › Article › peer-review
Open Access57 Scopus citations -
Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016
Clark, W. T., Kasak, L., Bakolitsa, C., Hu, Z., Andreoletti, G., Babbi, G., Bromberg, Y., Casadio, R., Dunbrack, R., Folkman, L., Ford, C. T., Jones, D., Katsonis, P., Kundu, K., Lichtarge, O., Martelli, P. L., Mooney, S. D., Nodzak, C., Pal, L. R. & Radivojac, P. & 13 others, , Sep 1 2019, In: Human Mutation. 40, 9, p. 1519-1529 11 p.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains
Modi, V. & Dunbrack, R. L., Dec 1 2019, In: Scientific Reports. 9, 1, 19790.Research output: Contribution to journal › Article › peer-review
Open Access81 Scopus citations -
Defining a new nomenclature for the structures of active and inactive kinases
Modi, V. & Dunbrack, R. L., Apr 2 2019, In: Proceedings of the National Academy of Sciences of the United States of America. 116, 14, p. 6818-6827 10 p.Research output: Contribution to journal › Article › peer-review
Open Access212 Scopus citations -
Interaction of germline variants in a family with a history of early-onset clear cell renal cell carcinoma
Nicolas, E., Demidova, E. V., Iqbal, W., Serebriiskii, I. G., Vlasenkova, R., Ghatalia, P., Zhou, Y., Rainey, K., Forman, A. F., Dunbrack, R. L., Golemis, E. A., Hall, M. J., Daly, M. B. & Arora, S., Jan 2019, In: Molecular Genetics and Genomic Medicine. 7, 3, p. e556 e556.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Protein modeling to assess the pathogenicity of rare variants of SERPINA1 in patients suspected of having Alpha 1 Antitrypsin Deficiency
Kueppers, F., Andrake, M. D., Xu, Q., Dunbrack, R. L., Kim, J. & Sanders, C. L., Jul 15 2019, In: BMC Medical Genetics. 20, 1, p. 125 125.Research output: Contribution to journal › Article › peer-review
Open Access16 Scopus citations -
2018
Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity
Rudolph, M. J., Vance, D. J., Kelow, S., Angalakurthi, S. K., Nguyen, S., Davis, S. A., Rong, Y., Middaugh, C. R., Weis, D. D., Dunbrack, R., Karanicolas, J. & Mantis, N. J., Jul 1 2018, In: Protein Engineering, Design and Selection. 31, 7-8, p. 277-287 11 p.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Mouse modeling and structural analysis of the p.G307S mutation in human cystathionine -synthase (CBS) reveal effects on CBS activity but not stability
Gupta, S., Kelow, S., Wang, L., Andrake, M. D., Dunbrack, R. L. & Kruger, W. D., Sep 7 2018, In: Journal of Biological Chemistry. 293, 36, p. 13921-13931 11 p.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
Plk2 Loss Commonly Occurs in Colorectal Carcinomas but not Adenomas: Relationship to mTOR Signaling
Matthew, E. M., Yang, Z., Peri, S., Andrake, M., Dunbrack, R., Ross, E. & El-Deiry, W. S., Mar 2018, In: Neoplasia (United States). 20, 3, p. 244-255 12 p.Research output: Contribution to journal › Article › peer-review
Open Access15 Scopus citations -
Role of a selecting ligand in shaping the murine γδ-TCR repertoire
Fahl, S. P., Coffey, F., Kain, L., Zarin, P., Dunbrack, R. L., Teyton, L., Zúñiga-Pflücker, J. C., Kappes, D. J. & Wiest, D. L., Feb 20 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 8, p. 1889-1894 6 p.Research output: Contribution to journal › Article › peer-review
Open Access33 Scopus citations -
RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
Adolf-Bryfogle, J., Kalyuzhniy, O., Kubitz, M., Weitzner, B. D., Hu, X., Adachi, Y., Schief, W. R. & Dunbrack, R. L., Apr 2018, In: PLoS Computational Biology. 14, 4, e1006112.Research output: Contribution to journal › Article › peer-review
Open Access147 Scopus citations -
2017
Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4
Xu, Q., Tang, Q., Katsonis, P., Lichtarge, O., Jones, D., Bovo, S., Babbi, G., Martelli, P. L., Casadio, R., Lee, G. R., Seok, C., Fenton, A. W. & Dunbrack, R. L., Sep 2017, In: Human Mutation. 38, 9, p. 1123-1131 9 p.Research output: Contribution to journal › Article › peer-review
Open Access15 Scopus citations -
BRCA2, EGFR, and NTRK mutations in mismatch repair-deficient colorectal cancers with MSH2 or MLH1 mutations
Deihimi, S., Lev, A., Slifker, M., Shagisultanova, E., Xu, Q., Jung, K., Vijayvergia, N., Ross, E. A., Xiu, J., Swensen, J., Gatalica, Z., Andrake, M., Dunbrack, R. L. & El-Deiry, W. S., 2017, In: Oncotarget. 8, 25, p. 39945-39962 18 p.Research output: Contribution to journal › Article › peer-review
Open Access29 Scopus citations -
Functional analysis of rare variants in mismatch repair proteins augments results from computation-based predictive methods
Arora, S., Nicolas, E., Hall, M. J., Dunbrack, R. L. & Golemis, E. A., Jul 3 2017, In: Cancer Biology and Therapy. 18, 7, p. 519-533 15 p.Research output: Contribution to journal › Article › peer-review
Open Access20 Scopus citations -
Modeling and docking of antibody structures with Rosetta
Dunbrack, R. L., Feb 1 2017, In: Nature Protocols. 12, 2, p. 401-416 16 p.Research output: Contribution to journal › Article › peer-review
220 Scopus citations -
Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI
Carraro, M., Minervini, G., Giollo, M., Bromberg, Y., Capriotti, E., Casadio, R., Dunbrack, R., Elefanti, L., Fariselli, P., Ferrari, C., Gough, J., Katsonis, P., Leonardi, E., Lichtarge, O., Menin, C., Martelli, P. L., Niroula, A., Pal, L. R., Repo, S. & Scaini, M. C. & 11 others, , Sep 2017, In: Human Mutation. 38, 9, p. 1042-1050 9 p.Research output: Contribution to journal › Article › peer-review
Open Access13 Scopus citations -
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O'Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., Labonte, J. W., Pacella, M. S., Bonneau, R., Bradley, P., Dunbrack, R. L., Das, R., Baker, D., Kuhlman, B., Kortemme, T. & Gray, J. J., Jun 13 2017, In: Journal of Chemical Theory and Computation. 13, 6, p. 3031-3048 18 p.Research output: Contribution to journal › Article › peer-review
968 Scopus citations -
2016
Assessment of refinement of template-based models in CASP11
Modi, V. & Dunbrack, R. L., 2016, In: Proteins: Structure, Function and Bioinformatics. 84, p. 260-281 22 p.Research output: Contribution to journal › Article › peer-review
Open Access36 Scopus citations -
Assessment of template-based modeling of protein structure in CASP11
Modi, V., Xu, Q., Adhikari, S. & Dunbrack, R. L., 2016, In: Proteins: Structure, Function and Bioinformatics. 84, p. 200-220 21 p.Research output: Contribution to journal › Article › peer-review
Open Access28 Scopus citations -
Biological function derived from predicted structures in CASP11
Huwe, P. J., Xu, Q., Shapovalov, M. V., Modi, V., Andrake, M. D. & Dunbrack, R. L., Sep 1 2016, In: Proteins: Structure, Function and Bioinformatics. 84, p. 370-391 22 p.Research output: Contribution to journal › Article › peer-review
8 Scopus citations -
CASP 11 target classification
Kinch, L. N., Li, W., Schaeffer, R. D., Dunbrack, R. L., Monastyrskyy, B., Kryshtafovych, A. & Grishin, N. V., Sep 1 2016, In: Proteins: Structure, Function and Bioinformatics. 84, p. 20-33 14 p.Research output: Contribution to journal › Article › peer-review
Open Access31 Scopus citations -
2015
Cancer signature investigation: ERBB2 (HER2)-activating mutation and amplification-positive breast carcinoma mimicking lung primary
Shih, J., Bashir, B., Gustafson, K. S., Andrake, M., Dunbrack, R. L., Goldstein, L. J. & Boumber, Y., Aug 1 2015, In: Journal of the National Comprehensive Cancer Network : JNCCN. 13, 8, p. 947-952 6 p.Research output: Contribution to journal › Article › peer-review
Open Access13 Scopus citations -
Characteristics of clinical trials that require participants to be fluent in English
Egleston, B. L., Pedraza, O., Wong, Y. N., Dunbrack, R. L., Griffin, C. L., Ross, E. A. & Beck, J. R., Dec 1 2015, In: Clinical Trials. 12, 6, p. 618-626 9 p.Research output: Contribution to journal › Article › peer-review
Open Access33 Scopus citations -
Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors
Vijayan, R. S. K., He, P., Modi, V., Duong-Ly, K. C., Ma, H., Peterson, J. R., Dunbrack, R. L. & Levy, R. M., Jan 8 2015, In: Journal of Medicinal Chemistry. 58, 1, p. 466-479 14 p.Research output: Contribution to journal › Article › peer-review
Open Access179 Scopus citations