Brian M. Baker - Publications

Chemistry and Biochemistry University of Notre Dame, Notre Dame, IN, United States 
molecular recognition and cellular communication

127 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Ahn YM, Maddumage JC, Grant EJ, Chatzileontiadou DSM, Perera WWJG, Baker BM, Szeto C, Gras S. The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific. Current Research in Structural Biology. 7: 100148. PMID 38742159 DOI: 10.1016/j.crstbi.2024.100148  0.504
2024 Rosenberg AM, Ayres CM, Medina-Cucurella AV, Whitehead TA, Baker BM. Enhanced T cell receptor specificity through framework engineering. Frontiers in Immunology. 15: 1345368. PMID 38545094 DOI: 10.3389/fimmu.2024.1345368  0.384
2024 Adams AC, Macy AM, Borden ES, Herrmann LM, Brambley CA, Ma T, Li X, Hughes A, Roe DJ, Mangold AR, Buetow KH, Wilson MA, Baker BM, Hastings KT. Distinct sets of molecular characteristics define tumor-rejecting neoantigens. Biorxiv : the Preprint Server For Biology. PMID 38405868 DOI: 10.1101/2024.02.13.579546  0.335
2023 Mikhaylov V, Brambley CA, Keller GLJ, Arbuiso AG, Weiss LI, Baker BM, Levine AJ. Accurate modeling of peptide-MHC structures with AlphaFold. Structure (London, England : 1993). PMID 38113889 DOI: 10.1016/j.str.2023.11.011  0.529
2023 Gillig MA, Brennick CA, George MM, Balsbaugh JL, Shcheglova TV, Mandoiu II, Rosales T, Baker BM, Srivastava PK, Karandikar SH. CD8+ T Cell-Dependent Antitumor Activity In Vivo of a Mass Spectrometry-Identified Neoepitope despite Undetectable CD8+ Immunogenicity In Vitro. Journal of Immunology (Baltimore, Md. : 1950). PMID 37966257 DOI: 10.4049/jimmunol.2300356  0.325
2023 Klebanoff CA, Chandran SS, Baker BM, Quezada SA, Ribas A. T cell receptor therapeutics: immunological targeting of the intracellular cancer proteome. Nature Reviews. Drug Discovery. PMID 37891435 DOI: 10.1038/s41573-023-00809-z  0.445
2023 Shi T, Burg AR, Caldwell JT, Roskin KM, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso JA, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, ... ... Baker BM, et al. Single cell transcriptomic analysis of renal allograft rejection reveals insights into intragraft TCR clonality. The Journal of Clinical Investigation. PMID 37227784 DOI: 10.1172/JCI170191  0.724
2023 Shi T, Burg AR, Caldwell JT, Roskin K, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso J, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, ... ... Baker BM, et al. Single cell transcriptomic analysis of renal allograft rejection reveals novel insights into intragraft TCR clonality. Biorxiv : the Preprint Server For Biology. PMID 36798151 DOI: 10.1101/2023.02.08.524808  0.705
2022 Singh NK, Alonso JA, Devlin JR, Keller GLJ, Gray GI, Chiranjivi AK, Foote SG, Landau LM, Arbuiso AG, Weiss LI, Rosenberg AM, Hellman LM, Nishimura MI, Baker BM. A class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry. Nature Communications. 13: 7189. PMID 36424374 DOI: 10.1038/s41467-022-34896-0  0.851
2022 Liu C, Liu H, Dasgupta M, Hellman LM, Zhang X, Qu K, Xue H, Wang Y, Fan F, Chang Q, Yu D, Ge L, Zhang Y, Cui Z, Zhang P, ... ... Baker BM, et al. Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma. Scientific Reports. 12: 12068. PMID 35840635 DOI: 10.1038/s41598-022-15946-5  0.669
2022 Ayres CM, Baker BM. Peptide-dependent tuning of major histocompatibility complex motional properties and the consequences for cellular immunity. Current Opinion in Immunology. 76: 102184. PMID 35550277 DOI: 10.1016/j.coi.2022.102184  0.558
2022 Keller GLJ, Weiss LI, Baker BM. Physicochemical Heuristics for Identifying High Fidelity, Near-Native Structural Models of Peptide/MHC Complexes. Frontiers in Immunology. 13: 887759. PMID 35547730 DOI: 10.3389/fimmu.2022.887759  0.529
2022 Chandran SS, Ma J, Klatt MG, Dündar F, Bandlamudi C, Razavi P, Wen HY, Weigelt B, Zumbo P, Fu SN, Banks LB, Yi F, Vercher E, Etxeberria I, Bestman WD, ... ... Baker BM, et al. Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA. Nature Medicine. PMID 35484264 DOI: 10.1038/s41591-022-01786-3  0.407
2022 Rosenberg AM, Baker BM. Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease. Current Opinion in Structural Biology. 74: 102358. PMID 35344834 DOI: 10.1016/  0.512
2022 Richards KA, Lavery C, Keller GLJ, Miller J, Baker BM, Sant AJ. A previously unappreciated polymorphism in the beta chain of I-A expressed in autoimmunity-prone SJL mice: Combined impact on antibody, CD4 T cell recognition and MHC class II dimer structural stability. Molecular Immunology. 143: 17-26. PMID 34995990 DOI: 10.1016/j.molimm.2021.12.022  0.436
2021 Pederson S, Biondi DM, Allan B, Cady R, Schaeffler B, Baker B, Latham J. Clinical Immunogenicity Evaluation of Eptinezumab, a Therapeutic Humanized Monoclonal Antibody Targeting Calcitonin Gene-Related Peptide (CGRP) for the Preventive Treatment of Migraine. Frontiers in Immunology. 12: 765822. PMID 34759933 DOI: 10.3389/fimmu.2021.765822  0.305
2021 Ebrahimi-Nik H, Moussa M, Englander RP, Singhaviranon S, Michaux J, Pak H, Miyadera H, Corwin WL, Keller GLJ, Hagymasi AT, Shcheglova TV, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, et al. Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope. Nature Communications. 12: 6423. PMID 34741035 DOI: 10.1038/s41467-021-26646-5  0.478
2021 Kaseke C, Park RJ, Singh NK, Koundakjian D, Bashirova A, Garcia Beltran WF, Takou Mbah OC, Ma J, Senjobe F, Urbach JM, Nathan A, Rossin EJ, Tano-Menka R, Khatri A, Piechocka-Trocha A, ... ... Baker BM, et al. HLA class-I-peptide stability mediates CD8 T cell immunodominance hierarchies and facilitates HLA-associated immune control of HIV. Cell Reports. 36: 109378. PMID 34260940 DOI: 10.1016/j.celrep.2021.109378  0.827
2021 Kaseke C, Park RJ, Singh NK, Koundakjian D, Bashirova A, Garcia Beltran WF, Takou Mbah OC, Ma J, Senjobe F, Urbach JM, Nathan A, Rossin EJ, Tano-Menka R, Khatri A, Piechocka-Trocha A, ... ... Baker BM, et al. HLA class-I-peptide stability mediates CD8 T cell immunodominance hierarchies and facilitates HLA-associated immune control of HIV. Cell Reports. 36: 109378. PMID 34260940 DOI: 10.1016/j.celrep.2021.109378  0.827
2021 Alonso JA, Smith AR, Baker BM. Tumor rejection properties of gp100-specific T cells correlate with T cell receptor binding affinity towards the wild type rather than anchor-modified antigen. Molecular Immunology. 135: 365-372. PMID 33990005 DOI: 10.1016/j.molimm.2021.05.001  0.838
2021 Ma J, Ayres CM, Hellman LM, Devlin JR, Baker BM. Dynamic allostery controls the peptide sensitivity of the Ly49C natural killer receptor. The Journal of Biological Chemistry. 100686. PMID 33891944 DOI: 10.1016/j.jbc.2021.100686  0.724
2021 Schmidt J, Smith AR, Magnin M, Racle J, Devlin JR, Bobisse S, Cesbron J, Bonnet V, Carmona SJ, Huber F, Ciriello G, Speiser DE, Bassani-Sternberg M, Coukos G, Baker BM, et al. Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting. Cell Reports. Medicine. 2: 100194. PMID 33665637 DOI: 10.1016/j.xcrm.2021.100194  0.456
2021 Smith AR, Alonso JA, Ayres CM, Singh NK, Hellman LM, Baker BM. Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33468649 DOI: 10.1073/pnas.2018125118  0.887
2020 Borrman T, Pierce BG, Vreven T, Baker BM, Weng Z. High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. Bioinformatics (Oxford, England). PMID 33355667 DOI: 10.1093/bioinformatics/btaa1050  0.527
2020 Singh NK, Alonso JA, Harris DT, Anderson SD, Ma J, Hellman LM, Rosenberg AM, Kolawole EM, Evavold BD, Kranz DM, Baker BM. An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes. Biochemistry. PMID 33074657 DOI: 10.1021/acs.biochem.0c00689  0.889
2020 Devlin JR, Alonso JA, Ayres CM, Keller GLJ, Bobisse S, Vander Kooi CW, Coukos G, Gfeller D, Harari A, Baker BM. Structural dissimilarity from self drives neoepitope escape from immune tolerance. Nature Chemical Biology. PMID 32807968 DOI: 10.1038/S41589-020-0610-1  0.811
2020 Tarbe M, Miles JJ, Edwards ESJ, Sewell AK, Baker BM, Quideau S. Synthesis and biological evaluation of hapten-clicked analogues of the antigenic peptide Melan-A/MART-126(27L)-35. Chemmedchem. PMID 32162475 DOI: 10.1002/Cmdc.202000038  0.623
2020 Baker B, Kranz D. Decision letter: Interrogating the recognition landscape of a conserved HIV-specific TCR reveals distinct bacterial peptide cross-reactivity Elife. DOI: 10.7554/Elife.58128.Sa1  0.433
2020 Groth E, Ayres CM, Baker BM, Corcelli SA. Modeling the Binding Mechanism of a T Cell Receptor and Major Histocompatibility Complex Biophysical Journal. 118: 245a. DOI: 10.1016/J.Bpj.2019.11.1435  0.504
2019 Spear TT, Evavold BD, Baker BM, Nishimura MI. Understanding TCR affinity, antigen specificity, and cross-reactivity to improve TCR gene-modified T cells for cancer immunotherapy. Cancer Immunology, Immunotherapy : Cii. PMID 31595324 DOI: 10.1007/S00262-019-02401-0  0.506
2019 Singh NK, Abualrous ET, Ayres CM, Noé F, Gowthaman R, Pierce BG, Baker BM. Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen. Proteins. PMID 31589793 DOI: 10.1002/Prot.25829  0.818
2019 Riley TP, Keller GLJ, Smith AR, Davancaze LM, Arbuiso AG, Devlin JR, Baker BM. Structure Based Prediction of Neoantigen Immunogenicity. Frontiers in Immunology. 10: 2047. PMID 31555277 DOI: 10.3389/Fimmu.2019.02047  0.816
2019 McGrath E, Waschbüsch D, Baker BM, Khan AR. LRRK2 binds to the Rab32 subfamily in a GTP-dependent manner its armadillo domain. Small Gtpases. 1-14. PMID 31552791 DOI: 10.1080/21541248.2019.1666623  0.303
2019 Ebrahimi-Nik H, Michaux J, Corwin WL, Keller GL, Shcheglova T, Pak H, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK. Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection. Jci Insight. 5. PMID 31219806 DOI: 10.1172/Jci.Insight.129152  0.382
2019 Ayres CM, Abualrous ET, Bailey A, Abraham C, Hellman LM, Corcelli SA, Noé F, Elliott T, Baker BM. Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility. Frontiers in Immunology. 10: 966. PMID 31130956 DOI: 10.3389/Fimmu.2019.00966  0.77
2019 Chandran S, Ma J, Klatt MG, Dündar F, Zumbo P, Femia MR, Betel D, Scheinberg DA, Baker BM, Klebanoff CA. Abstract CN01-03: T cell receptor gene therapy for a public neoantigen derived from mutated PIK3CA, a dominant driver oncogene in breast and endometrial cancers Molecular Cancer Therapeutics. 18. DOI: 10.1158/1535-7163.Targ-19-Cn01-03  0.479
2019 Devlin J, Bobisse S, Harari A, Baker B. 3348 Structural Determinants of Neoantigen Immunogenicity for Cancer Therapy Journal of Clinical and Translational Science. 3: 22-22. DOI: 10.1017/cts.2019.54  0.365
2018 Hellman LM, Foley KC, Singh NK, Alonso JA, Riley TP, Devlin JR, Ayres CM, Keller GLJ, Zhang Y, Vander Kooi CW, Nishimura MI, Baker BM. Improving T Cell Receptor On-Target Specificity via Structure-Guided Design. Molecular Therapy : the Journal of the American Society of Gene Therapy. PMID 30617019 DOI: 10.1016/J.Ymthe.2018.12.010  0.85
2018 Riley TP, Baker BM. The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics. Seminars in Cell & Developmental Biology. 84: 30-41. PMID 30449534 DOI: 10.1016/J.Semcdb.2017.10.017  0.775
2018 Riley TP, Hellman LM, Gee MH, Mendoza JL, Alonso JA, Foley KC, Nishimura MI, Vander Kooi CW, Garcia KC, Baker BM. T cell receptor cross-reactivity expanded by dramatic peptide-MHC adaptability. Nature Chemical Biology. 14: 934-942. PMID 30224695 DOI: 10.1038/S41589-018-0130-4  0.872
2018 Eby JM, Smith AR, Riley TP, Cosgrove C, Ankney CM, Henning SW, Paulos CM, Garrett-Mayer E, Luiten RM, Nishimura MI, Baker BM, Le Poole IC. Molecular properties of gp100-reactive T cell receptors drive the cytokine profile and antitumor efficacy of transgenic host T cells. Pigment Cell & Melanoma Research. PMID 30009548 DOI: 10.1111/Pcmr.12724  0.796
2018 Spear TT, Wang Y, Smith TW, Simms PE, Garrett-Mayer E, Hellman LM, Baker BM, Nishimura MI. Altered Peptide Ligands Impact the Diversity of Polyfunctional Phenotypes in T Cell Receptor Gene-Modified T Cells. Molecular Therapy : the Journal of the American Society of Gene Therapy. PMID 29503203 DOI: 10.1016/J.Ymthe.2018.01.015  0.741
2018 Baker BM. Accounting for Specificity and Cross-Reactivity in T Cell Receptor Molecular Recognition Biophysical Journal. 114: 219a. DOI: 10.1016/J.Bpj.2017.11.1220  0.469
2017 Moore T, Wagner CR, Scurti GM, Hutchens KA, Godellas C, Clark AL, Kolawole EM, Hellman LM, Singh NK, Huyke FA, Wang SY, Calabrese KM, Embree HD, Orentas R, Shirai K, ... ... Baker BM, et al. Correction to: Clinical and immunologic evaluation of three metastatic melanoma patients treated with autologous melanoma-reactive TCR-transduced T cells. Cancer Immunology, Immunotherapy : Cii. PMID 29264697 DOI: 10.1007/S00262-017-2102-Z  0.732
2017 Moore T, Wagner CR, Scurti GM, Hutchens KA, Godellas C, Clark AL, Kolawole EM, Hellman LM, Singh NK, Huyke FA, Wang SY, Calabrese KM, Embree HD, Orentas R, Shirai K, ... ... Baker BM, et al. Clinical and immunologic evaluation of three metastatic melanoma patients treated with autologous melanoma-reactive TCR-transduced T cells. Cancer Immunology, Immunotherapy : Cii. PMID 29052782 DOI: 10.1007/S00262-017-2073-0  0.742
2017 Singh NK, Riley TP, Baker SCB, Borrman T, Weng Z, Baker BM. Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes. Journal of Immunology (Baltimore, Md. : 1950). 199: 2203-2213. PMID 28923982 DOI: 10.4049/Jimmunol.1700744  0.847
2017 Ayres CM, Corcelli SA, Baker BM. Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings. Frontiers in Immunology. 8: 935. PMID 28824655 DOI: 10.3389/Fimmu.2017.00935  0.582
2017 Ayres CM, Riley TP, Corcelli SA, Baker BM. Modeling Sequence Dependent Peptide Fluctuations in Immunologic Recognition. Journal of Chemical Information and Modeling. PMID 28696685 DOI: 10.1021/Acs.Jcim.7B00118  0.797
2017 Spear TT, Wang Y, Foley KC, Murray DC, Scurti GM, Simms PE, Garrett-Mayer E, Hellman LM, Baker BM, Nishimura MI. Critical biological parameters modulate affinity as a determinant of function in T-cell receptor gene-modified T-cells. Cancer Immunology, Immunotherapy : Cii. PMID 28634816 DOI: 10.1007/S00262-017-2032-9  0.729
2017 Wang Y, Singh NK, Spear TT, Hellman LM, Piepenbrink KH, McMahan RH, Rosen HR, Vander Kooi CW, Nishimura MI, Baker BM. How an alloreactive T-cell receptor achieves peptide and MHC specificity. Proceedings of the National Academy of Sciences of the United States of America. PMID 28572406 DOI: 10.1073/Pnas.1700459114  0.849
2017 Blevins SJ, Baker BM. Using Global Analysis to Extend the Accuracy and Precision of Binding Measurements with T cell Receptors and Their Peptide/MHC Ligands. Frontiers in Molecular Biosciences. 4: 2. PMID 28197404 DOI: 10.3389/Fmolb.2017.00002  0.878
2017 Borrman T, Cimons J, Cosiano M, Purcaro M, Pierce BG, Baker BM, Weng Z. ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes. Proteins. PMID 28160322 DOI: 10.1002/Prot.25260  0.557
2017 Riley TP, Mendoza J, Garcia KC, Baker BM. 2064 Journal of Clinical and Translational Science. 1: 54-55. DOI: 10.1017/cts.2017.195  0.815
2016 Baker BM, Evavold BD. MHC Bias by T Cell Receptors: Genetic Evidence for MHC and TCR Coevolution. Trends in Immunology. PMID 27939452 DOI: 10.1016/J.It.2016.11.003  0.519
2016 Singh NK, Baker BM. Ligand-Driven T Cell Receptor Selection in Celiac Disease. Structure (London, England : 1993). 24: 1623-1624. PMID 27705812 DOI: 10.1016/J.Str.2016.09.004  0.71
2016 Harris DT, Wang N, Riley TP, Anderson SD, Singh NK, Procko E, Baker BM, Kranz DM. Deep mutational scans as a guide to engineering high-affinity T cell receptor interactions with peptide-bound MHC. The Journal of Biological Chemistry. PMID 27681597 DOI: 10.1074/Jbc.M116.748681  0.829
2016 Riley TP, Ayres CM, Hellman LM, Singh NK, Cosiano M, Cimons JM, Anderson MJ, Piepenbrink KH, Pierce BG, Weng Z, Baker BM. A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Engineering, Design & Selection : Peds. PMID 27624308 DOI: 10.1093/Protein/Gzw050  0.835
2016 Harris DT, Singh NK, Cai Q, Smith SN, Vander Kooi CW, Procko E, Kranz DM, Baker BM. An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry. Structure (London, England : 1993). PMID 27238970 DOI: 10.1016/J.Str.2016.04.011  0.766
2016 Ayres CM, Scott DR, Corcelli SA, Baker BM. Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity. Scientific Reports. 6: 25070. PMID 27118724 DOI: 10.1038/Srep25070  0.725
2016 Riley TP, Singh NK, Pierce BG, Weng Z, Baker BM. Computational Modeling of T Cell Receptor Complexes. Methods in Molecular Biology (Clifton, N.J.). 1414: 319-40. PMID 27094300 DOI: 10.1007/978-1-4939-3569-7_19  0.842
2016 Riley TP, Singh NK, Pierce BG, Baker BM, Weng Z. Computational Reprogramming of T Cell Antigen Receptor Binding Properties. Methods in Molecular Biology (Clifton, N.J.). 1414: 305-18. PMID 27094299 DOI: 10.1007/978-1-4939-3569-7_18  0.867
2016 Spear TT, Riley TP, Lyons GE, Callender GG, Roszkowski JJ, Wang Y, Simms PE, Scurti GM, Foley KC, Murray DC, Hellman LM, McMahan RH, Iwashima M, Garrett-Mayer E, Rosen HR, ... Baker BM, et al. Hepatitis C virus-cross-reactive TCR gene-modified T cells: a model for immunotherapy against diseases with genomic instability. Journal of Leukocyte Biology. PMID 26921345 DOI: 10.1189/Jlb.2A1215-561R  0.824
2016 Hellman LM, Yin L, Wang Y, Blevins SJ, Riley TP, Belden OS, Spear TT, Nishimura MI, Stern LJ, Baker BM. Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes. Journal of Immunological Methods. PMID 26906089 DOI: 10.1016/J.Jim.2016.02.016  0.832
2016 Blevins SJ, Pierce BG, Singh NK, Riley TP, Wang Y, Spear TT, Nishimura MI, Weng Z, Baker BM. How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire. Proceedings of the National Academy of Sciences of the United States of America. PMID 26884163 DOI: 10.1073/Pnas.1522069113  0.841
2015 Thompson MG, Larson M, Vidrine A, Barrios K, Navarro F, Meyers K, Simms P, Prajapati K, Chitsike L, Hellman LM, Baker BM, Watkins SK. FOXO3-NF-κB RelA Protein Complexes Reduce Proinflammatory Cell Signaling and Function. Journal of Immunology (Baltimore, Md. : 1950). PMID 26561547 DOI: 10.4049/Jimmunol.1501758  0.591
2015 Adams JJ, Narayanan S, Birnbaum ME, Sidhu SS, Blevins SJ, Gee MH, Sibener LV, Baker BM, Kranz DM, Garcia KC. Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity. Nature Immunology. PMID 26523866 DOI: 10.1038/Ni.3310  0.874
2014 Smith SN, Wang Y, Baylon JL, Singh NK, Baker BM, Tajkhorshid E, Kranz DM. Changing the peptide specificity of a human T-cell receptor by directed evolution. Nature Communications. 5: 5223. PMID 25376839 DOI: 10.1038/Ncomms6223  0.811
2014 Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM, Mandoiu II, Srivastava PK. Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity. The Journal of Experimental Medicine. 211: 2231-48. PMID 25245761 DOI: 10.1084/jem.20141308  0.389
2014 Pierce BG, Hellman LM, Hossain M, Singh NK, Vander Kooi CW, Weng Z, Baker BM. Computational design of the affinity and specificity of a therapeutic T cell receptor. Plos Computational Biology. 10: e1003478. PMID 24550723 DOI: 10.1371/Journal.Pcbi.1003478  0.878
2014 Hawse WF, De S, Greenwood AI, Nicholson LK, Zajicek J, Kovrigin EL, Kranz DM, Garcia KC, Baker BM. TCR scanning of peptide/MHC through complementary matching of receptor and ligand molecular flexibility. Journal of Immunology (Baltimore, Md. : 1950). 192: 2885-91. PMID 24523505 DOI: 10.4049/Jimmunol.1302953  0.836
2014 Pierce BG, Hellman LM, Hossain M, Singh NK, Kooi CWV, Weng Z, Baker BM. Scores from ZAFFI (ZF) and Rosetta (Ros), predicted peptide contacts, and measured energies (in kcal/mol) for DMF5 point mutants binding to ELA/HLA-A2 and AAG/HLA-A2. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1003478.T002  0.83
2013 Smith SN, Sommermeyer D, Piepenbrink KH, Blevins SJ, Bernhard H, Uckert W, Baker BM, Kranz DM. Plasticity in the contribution of T cell receptor variable region residues to binding of peptide-HLA-A2 complexes. Journal of Molecular Biology. 425: 4496-507. PMID 23954306 DOI: 10.1016/J.Jmb.2013.08.007  0.863
2013 Hawse WF, Gloor BE, Ayres CM, Kho K, Nuter E, Baker BM. Peptide modulation of class I major histocompatibility complex protein molecular flexibility and the implications for immune recognition. The Journal of Biological Chemistry. 288: 24372-81. PMID 23836912 DOI: 10.1074/Jbc.M113.490664  0.871
2013 Cole DK, Sami M, Scott DR, Rizkallah PJ, Borbulevych OY, Todorov PT, Moysey RK, Jakobsen BK, Boulter JM, Baker BM, Yi Li. Increased Peptide Contacts Govern High Affinity Binding of a Modified TCR Whilst Maintaining a Native pMHC Docking Mode. Frontiers in Immunology. 4: 168. PMID 23805144 DOI: 10.3389/Fimmu.2013.00168  0.858
2013 Piepenbrink KH, Blevins SJ, Scott DR, Baker BM. The basis for limited specificity and MHC restriction in a T cell receptor interface. Nature Communications. 4: 1948. PMID 23736024 DOI: 10.1038/Ncomms2948  0.875
2013 Madura F, Rizkallah PJ, Miles KM, Holland CJ, Bulek AM, Fuller A, Schauenburg AJ, Miles JJ, Liddy N, Sami M, Li Y, Hossain M, Baker BM, Jakobsen BK, Sewell AK, et al. T-cell receptor specificity maintained by altered thermodynamics. The Journal of Biological Chemistry. 288: 18766-75. PMID 23698002 DOI: 10.1074/Jbc.M113.464560  0.81
2013 Baker BM, Piepenbrink KH, Blevins SJ. T Cell Receptor Specificity, Cross-Reactivity, and MHC Restriction are Inextricably Linked and Result from Cooperative Engagement of the Composite Peptide/MHC Surface Biophysical Journal. 104: 403a. DOI: 10.1016/J.Bpj.2012.11.2249  0.882
2012 Scott DR, Vardeman CF, Corcelli SA, Baker BM. Limitations of time-resolved fluorescence suggested by molecular simulations: assessing the dynamics of T cell receptor binding loops. Biophysical Journal. 103: 2532-40. PMID 23260055 DOI: 10.1016/J.Bpj.2012.10.037  0.646
2012 Baker BM, Scott DR, Blevins SJ, Hawse WF. Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism. Immunological Reviews. 250: 10-31. PMID 23046120 DOI: 10.1111/J.1600-065X.2012.01165.X  0.877
2012 Ekeruche-Makinde J, Clement M, Cole DK, Edwards ES, Ladell K, Miles JJ, Matthews KK, Fuller A, Lloyd KA, Madura F, Dolton GM, Pentier J, Lissina A, Gostick E, Baxter TK, ... Baker BM, et al. T-cell receptor-optimized peptide skewing of the T-cell repertoire can enhance antigen targeting. The Journal of Biological Chemistry. 287: 37269-81. PMID 22952231 DOI: 10.1074/Jbc.M112.386409  0.609
2012 Hawse WF, Champion MM, Joyce MV, Hellman LM, Hossain M, Ryan V, Pierce BG, Weng Z, Baker BM. Cutting edge: Evidence for a dynamically driven T cell signaling mechanism. Journal of Immunology (Baltimore, Md. : 1950). 188: 5819-23. PMID 22611242 DOI: 10.4049/Jimmunol.1200952  0.848
2012 Kumarasiri M, Llarrull LI, Borbulevych O, Fishovitz J, Lastochkin E, Baker BM, Mobashery S. An amino acid position at crossroads of evolution of protein function: antibiotic sensor domain of BlaR1 protein from Staphylococcus aureus versus clasS D β-lactamases. The Journal of Biological Chemistry. 287: 8232-41. PMID 22262858 DOI: 10.1074/Jbc.M111.333179  0.637
2012 Aggen DH, Chervin AS, Schmitt TM, Engels B, Stone JD, Richman SA, Piepenbrink KH, Baker BM, Greenberg PD, Schreiber H, Kranz DM. Single-chain VαVβ T-cell receptors function without mispairing with endogenous TCR chains. Gene Therapy. 19: 365-74. PMID 21753797 DOI: 10.1038/Gt.2011.104  0.777
2011 Scott DR, Borbulevych OY, Piepenbrink KH, Corcelli SA, Baker BM. Disparate degrees of hypervariable loop flexibility control T-cell receptor cross-reactivity, specificity, and binding mechanism. Journal of Molecular Biology. 414: 385-400. PMID 22019736 DOI: 10.1016/J.Jmb.2011.10.006  0.869
2011 Insaidoo FK, Borbulevych OY, Hossain M, Santhanagopolan SM, Baxter TK, Baker BM. Loss of T cell antigen recognition arising from changes in peptide and major histocompatibility complex protein flexibility: implications for vaccine design. The Journal of Biological Chemistry. 286: 40163-73. PMID 21937447 DOI: 10.1074/jbc.M111.283564  0.871
2011 Borbulevych OY, Santhanagopolan SM, Hossain M, Baker BM. TCRs used in cancer gene therapy cross-react with MART-1/Melan-A tumor antigens via distinct mechanisms. Journal of Immunology (Baltimore, Md. : 1950). 187: 2453-63. PMID 21795600 DOI: 10.4049/Jimmunol.1101268  0.831
2011 Borbulevych O, Kumarasiri M, Wilson B, Llarrull LI, Lee M, Hesek D, Shi Q, Peng J, Baker BM, Mobashery S. Lysine Nzeta-decarboxylation switch and activation of the beta-lactam sensor domain of BlaR1 protein of methicillin-resistant Staphylococcus aureus. The Journal of Biological Chemistry. 286: 31466-72. PMID 21775440 DOI: 10.1074/Jbc.M111.252189  0.607
2011 Borbulevych OY, Piepenbrink KH, Baker BM. Conformational melding permits a conserved binding geometry in TCR recognition of foreign and self molecular mimics. Journal of Immunology (Baltimore, Md. : 1950). 186: 2950-8. PMID 21282516 DOI: 10.4049/Jimmunol.1003150  0.852
2011 Aggen DH, Chervin AS, Insaidoo FK, Piepenbrink KH, Baker BM, Kranz DM. Identification and engineering of human variable regions that allow expression of stable single-chain T cell receptors. Protein Engineering, Design & Selection : Peds. 24: 361-72. PMID 21159619 DOI: 10.1093/Protein/Gzq113  0.802
2011 Piepenbrink KH, Baker BM. The Binding Energetics of a T-Cell Receptor Show a Bias Toward the Conserved Antigen Presentation Molecule, HLA Biophysical Journal. 100: 527a. DOI: 10.1016/J.Bpj.2010.12.3082  0.855
2010 Tarbe M, Azcune I, Balentová E, Miles JJ, Edwards EE, Miles KM, Do P, Baker BM, Sewell AK, Aizpurua JM, Douat-Casassus C, Quideau S. Design, synthesis and evaluation of β-lactam antigenic peptide hybrids; unusual opening of the β-lactam ring in acidic media. Organic & Biomolecular Chemistry. 8: 5345-53. PMID 20927455 DOI: 10.1039/C003877F  0.577
2010 Douat-Casassus C, Borbulevych O, Tarbe M, Gervois N, Jotereau F, Baker BM, Quideau S. Crystal structures of HLA-A*0201 complexed with Melan-A/MART-1(26(27L)-35) peptidomimetics reveal conformational heterogeneity and highlight degeneracy of T cell recognition. Journal of Medicinal Chemistry. 53: 7061-6. PMID 20806940 DOI: 10.1021/Jm100683P  0.777
2010 Borbulevych OY, Do P, Baker BM. Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A*0201: implications for WT1-based cancer therapeutics. Molecular Immunology. 47: 2519-24. PMID 20619457 DOI: 10.1016/J.Molimm.2010.06.005  0.797
2009 Piepenbrink KH, Gloor BE, Armstrong KM, Baker BM. Methods for quantifying T cell receptor binding affinities and thermodynamics. Methods in Enzymology. 466: 359-81. PMID 21609868 DOI: 10.1016/S0076-6879(09)66015-8  0.867
2009 Borbulevych OY, Piepenbrink KH, Gloor BE, Scott DR, Sommese RF, Cole DK, Sewell AK, Baker BM. T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility. Immunity. 31: 885-96. PMID 20064447 DOI: 10.1016/J.Immuni.2009.11.003  0.856
2009 Insaidoo FK, Zajicek J, Baker BM. A general and efficient approach for NMR studies of peptide dynamics in class I MHC peptide binding grooves. Biochemistry. 48: 9708-10. PMID 19772349 DOI: 10.1021/Bi9008787  0.871
2009 Piepenbrink KH, Borbulevych OY, Sommese RF, Clemens J, Armstrong KM, Desmond C, Do P, Baker BM. Fluorine substitutions in an antigenic peptide selectively modulate T-cell receptor binding in a minimally perturbing manner. The Biochemical Journal. 423: 353-61. PMID 19698083 DOI: 10.1042/Bj20090732  0.891
2009 Bowerman NA, Crofts TS, Chlewicki L, Do P, Baker BM, Christopher Garcia K, Kranz DM. Engineering the binding properties of the T cell receptor:peptide:MHC ternary complex that governs T cell activity. Molecular Immunology. 46: 3000-8. PMID 19595460 DOI: 10.1016/J.Molimm.2009.06.012  0.536
2009 Chen H, Piechocka-Trocha A, Miura T, Brockman MA, Julg BD, Baker BM, Rothchild AC, Block BL, Schneidewind A, Koibuchi T, Pereyra F, Allen TM, Walker BD. Differential neutralization of human immunodeficiency virus (HIV) replication in autologous CD4 T cells by HIV-specific cytotoxic T lymphocytes. Journal of Virology. 83: 3138-49. PMID 19158248 DOI: 10.1128/Jvi.02073-08  0.5
2008 Armstrong KM, Piepenbrink KH, Baker BM. Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes. The Biochemical Journal. 415: 183-96. PMID 18800968 DOI: 10.1042/Bj20080850  0.864
2008 Miura T, Brockman MA, Brumme CJ, Brumme ZL, Carlson JM, Pereyra F, Trocha A, Addo MM, Block BL, Rothchild AC, Baker BM, Flynn T, Schneidewind A, Li B, Wang YE, et al. Genetic characterization of human immunodeficiency virus type 1 in elite controllers: lack of gross genetic defects or common amino acid changes. Journal of Virology. 82: 8422-30. PMID 18562530 DOI: 10.1128/Jvi.00535-08  0.364
2008 Armstrong KM, Insaidoo FK, Baker BM. Thermodynamics of T-cell receptor-peptide/MHC interactions: progress and opportunities. Journal of Molecular Recognition : Jmr. 21: 275-87. PMID 18496839 DOI: 10.1002/Jmr.896  0.861
2008 Loaiza A, Armstrong KM, Baker BM, Abu-Omar MM. Kinetics of thermal unfolding of phenylalanine hydroxylase variants containing different metal cofactors (FeII, CoII, and ZnII) and their isokinetic relationship. Inorganic Chemistry. 47: 4877-83. PMID 18433092 DOI: 10.1021/Ic800181Q  0.645
2007 Borbulevych OY, Insaidoo FK, Baxter TK, Powell DJ, Johnson LA, Restifo NP, Baker BM. Structures of MART-126/27-35 Peptide/HLA-A2 complexes reveal a remarkable disconnect between antigen structural homology and T cell recognition. Journal of Molecular Biology. 372: 1123-36. PMID 17719062 DOI: 10.1016/J.Jmb.2007.07.025  0.883
2007 Armstrong KM, Baker BM. A comprehensive calorimetric investigation of an entropically driven T cell receptor-peptide/major histocompatibility complex interaction. Biophysical Journal. 93: 597-609. PMID 17449678 DOI: 10.1529/Biophysj.107.104570  0.799
2007 Davis-Harrison RL, Insaidoo FK, Baker BM. T cell receptor binding transition states and recognition of peptide/MHC. Biochemistry. 46: 1840-50. PMID 17249694 DOI: 10.1021/Bi061702P  0.854
2006 Gagnon SJ, Borbulevych OY, Davis-Harrison RL, Turner RV, Damirjian M, Wojnarowicz A, Biddison WE, Baker BM. T cell receptor recognition via cooperative conformational plasticity. Journal of Molecular Biology. 363: 228-43. PMID 16962135 DOI: 10.1016/J.Jmb.2006.08.045  0.879
2005 Gagnon SJ, Borbulevych OY, Davis-Harrison RL, Baxter TK, Clemens JR, Armstrong KM, Turner RV, Damirjian M, Biddison WE, Baker BM. Unraveling a hotspot for TCR recognition on HLA-A2: evidence against the existence of peptide-independent TCR binding determinants. Journal of Molecular Biology. 353: 556-73. PMID 16197958 DOI: 10.1016/J.Jmb.2005.08.024  0.874
2005 Borbulevych OY, Baxter TK, Yu Z, Restifo NP, Baker BM. Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design. Journal of Immunology (Baltimore, Md. : 1950). 174: 4812-20. PMID 15814707 DOI: 10.4049/Jimmunol.174.8.4812  0.762
2005 Davis-Harrison RL, Armstrong KM, Baker BM. Two different T cell receptors use different thermodynamic strategies to recognize the same peptide/MHC ligand. Journal of Molecular Biology. 346: 533-50. PMID 15670602 DOI: 10.1016/J.Jmb.2004.11.063  0.861
2005 Davis-Harrison RL, Armstrong KM, Baker BM. Corrigendum to “Two Different T Cell Receptors use Different Thermodynamic Strategies to Recognize the Same Peptide/MHC Ligand” [J. Mol. Biol. (2005) 346, 533–550] Journal of Molecular Biology. 349: 906. DOI: 10.1016/J.Jmb.2005.04.038  0.861
2004 Yu Z, Theoret MR, Touloukian CE, Surman DR, Garman SC, Feigenbaum L, Baxter TK, Baker BM, Restifo NP. Poor immunogenicity of a self/tumor antigen derives from peptide-MHC-I instability and is independent of tolerance. The Journal of Clinical Investigation. 114: 551-9. PMID 15314692 DOI: 10.1172/Jci21695  0.768
2004 Swalley SE, Baker BM, Calder LJ, Harrison SC, Skehel JJ, Wiley DC. Full-length influenza hemagglutinin HA2 refolds into the trimeric low-pH-induced conformation. Biochemistry. 43: 5902-11. PMID 15134464 DOI: 10.1021/Bi049807K  0.539
2004 Baxter TK, Gagnon SJ, Davis-Harrison RL, Beck JC, Binz AK, Turner RV, Biddison WE, Baker BM. Strategic mutations in the class I major histocompatibility complex HLA-A2 independently affect both peptide binding and T cell receptor recognition. The Journal of Biological Chemistry. 279: 29175-84. PMID 15131131 DOI: 10.1074/Jbc.M403372200  0.865
2003 Binz AK, Rodriguez RC, Biddison WE, Baker BM. Thermodynamic and kinetic analysis of a peptide-class I MHC interaction highlights the noncovalent nature and conformational dynamics of the class I heterotrimer. Biochemistry. 42: 4954-61. PMID 12718537 DOI: 10.1021/Bi034077M  0.565
2002 Wang Z, Turner R, Baker BM, Biddison WE. MHC allele-specific molecular features determine peptide/HLA-A2 conformations that are recognized by HLA-A2-restricted T cell receptors. Journal of Immunology (Baltimore, Md. : 1950). 169: 3146-54. PMID 12218132 DOI: 10.4049/Jimmunol.169.6.3146  0.567
2001 Baker BM, Wiley DC. alpha beta T cell receptor ligand-specific oligomerization revisited. Immunity. 14: 681-92. PMID 11420039 DOI: 10.1016/S1074-7613(01)00160-1  0.6
2001 Baker BM, Turner RV, Gagnon SJ, Wiley DC, Biddison WE. Identification of a crucial energetic footprint on the alpha1 helix of human histocompatibility leukocyte antigen (HLA)-A2 that provides functional interactions for recognition by tax peptide/HLA-A2-specific T cell receptors. The Journal of Experimental Medicine. 193: 551-62. PMID 11238586 DOI: 10.1084/Jem.193.5.551  0.665
2000 Baker BM, Gagnon SJ, Biddison WE, Wiley DC. Conversion of a T cell antagonist into an agonist by repairing a defect in the TCR/peptide/MHC interface: implications for TCR signaling. Immunity. 13: 475-84. PMID 11070166 DOI: 10.1016/S1074-7613(00)00047-9  0.701
2000 Edgcomb SP, Baker BM, Murphy KP. The energetics of phosphate binding to a protein complex. Protein Science : a Publication of the Protein Society. 9: 927-33. PMID 10850802 DOI: 10.1110/Ps.9.5.927  0.812
2000 Khan AR, Baker BM, Ghosh P, Biddison WE, Wiley DC. The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site. Journal of Immunology (Baltimore, Md. : 1950). 164: 6398-405. PMID 10843695 DOI: 10.4049/Jimmunol.164.12.6398  0.786
1999 Baker BM, Ding YH, Garboczi DN, Biddison WE, Wiley DC. Structural, biochemical, and biophysical studies of HLA-A2/altered peptide ligands binding to viral-peptide-specific human T-cell receptors. Cold Spring Harbor Symposia On Quantitative Biology. 64: 235-41. PMID 11232291 DOI: 10.1101/Sqb.1999.64.235  0.75
1999 Ding YH, Baker BM, Garboczi DN, Biddison WE, Wiley DC. Four A6-TCR/peptide/HLA-A2 structures that generate very different T cell signals are nearly identical. Immunity. 11: 45-56. PMID 10435578 DOI: 10.1016/S1074-7613(00)80080-1  0.72
1999 Murphy KP, Baker BM, Edgcomb SP, Horn JR. Structural energetics of serine protease inhibition Pure and Applied Chemistry. 71: 1207-1213. DOI: 10.1351/Pac199971071207  0.792
1998 Baker BM, Murphy KP. Prediction of binding energetics from structure using empirical parameterization. Methods in Enzymology. 295: 294-315. PMID 9750224 DOI: 10.1016/S0076-6879(98)95045-5  0.594
1997 Baker BM, Murphy KP. Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase. Journal of Molecular Biology. 268: 557-69. PMID 9159490 DOI: 10.1006/Jmbi.1997.0977  0.577
1996 Baker BM, Murphy KP. Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry. Biophysical Journal. 71: 2049-55. PMID 8889179 DOI: 10.1016/S0006-3495(96)79403-1  0.543
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