Brian G. Pierce, Ph.D. - Publications

Affiliations: 
2008 Boston University, Boston, MA, United States 
Area:
Biostatistics Biology

66 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 Ribeiro-Filho HV, Jara GE, Guerra JVS, Cheung M, Felbinger NR, Pereira JGC, Pierce BG, Lopes-de-Oliveira PS. Exploring the Potential of Structure-Based Deep Learning Approaches for T cell Receptor Design. Biorxiv : the Preprint Server For Biology. PMID 38712216 DOI: 10.1101/2024.04.19.590222  0.3
2024 Azzam T, Du JJ, Flowers MW, Ali AV, Hunn JC, Vijayvargiya N, Knagaram R, Bogacz M, Maravillas KE, Sastre DE, Fields JK, Mirzaei A, Pierce BG, Sundberg EJ. Combinatorially restricted computational design of protein-protein interfaces to produce IgG heterodimers. Science Advances. 10: eadk8157. PMID 38598628 DOI: 10.1126/sciadv.adk8157  0.307
2023 Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, ... ... Pierce BG, et al. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins. PMID 37905971 DOI: 10.1002/prot.26609  0.362
2022 Yin R, Feng BY, Varshney A, Pierce BG. Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants. Protein Science : a Publication of the Protein Society. 31: e4379. PMID 35900023 DOI: 10.1002/pro.4379  0.435
2021 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, ... ... Pierce BG, et al. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins. PMID 34453465 DOI: 10.1002/prot.26222  0.318
2021 Guest JD, Vreven T, Zhou J, Moal I, Jeliazkov JR, Gray JJ, Weng Z, Pierce BG. An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants. Structure (London, England : 1993). PMID 33539768 DOI: 10.1016/j.str.2021.01.005  0.531
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  0.451
2020 Gowthaman R, Guest JD, Yin R, Adolf-Bryfogle J, Schief WR, Pierce BG. CoV3D: a database of high resolution coronavirus protein structures. Nucleic Acids Research. PMID 32890396 DOI: 10.1093/Nar/Gkaa731  0.416
2020 Pierce BG, Keck ZY, Wang R, Lau P, Garagusi K, Elkholy K, Toth EA, Urbanowicz RA, Guest JD, Agnihotri P, Kerzic MC, Marin A, Andrianov AK, Ball JK, Mariuzza RA, et al. Structure-based design of hepatitis C virus E2 glycoprotein improves serum binding and cross-neutralization. Journal of Virology. PMID 32878891 DOI: 10.1128/Jvi.00704-20  0.316
2020 Wu D, Gallagher DT, Gowthaman R, Pierce BG, Mariuzza RA. Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen. Nature Communications. 11: 2908. PMID 32518267 DOI: 10.1038/S41467-020-16755-Y  0.307
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Pierce BG, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.312
2020 Gowthaman R, Pierce BG. Modeling and Viewing T Cell Receptors Using TCRmodel and TCR3d. Methods in Molecular Biology (Clifton, N.J.). 2120: 197-212. PMID 32124321 DOI: 10.1007/978-1-0716-0327-7_14  0.374
2019 Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, ... ... Pierce BG, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838  0.623
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  0.357
2019 Gowthaman R, Pierce BG. TCR3d: The T cell receptor structural repertoire database. Bioinformatics (Oxford, England). PMID 31240309 DOI: 10.1093/Bioinformatics/Btz517  0.405
2019 Urbanowicz RA, Wang R, Schiel JE, Keck ZY, Kerzic MC, Lau P, Rangarajan S, Garagusi KJ, Tan L, Guest JD, Ball JK, Pierce BG, Mariuzza RA, Foung SKH, Fuerst TR. Antigenicity and Immunogenicity of Differentially Glycosylated HCV E2 Envelope Proteins Expressed in Mammalian and Insect Cells. Journal of Virology. PMID 30651366 DOI: 10.1128/Jvi.01403-18  0.329
2018 Rangarajan S, He Y, Chen Y, Kerzic MC, Ma B, Gowthaman R, Pierce BG, Nussinov R, Mariuzza RA, Orban J. Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites. The Journal of Biological Chemistry. PMID 30135211 DOI: 10.1074/Jbc.Ra118.003832  0.326
2018 Guest JD, Pierce BG. Computational Modeling of Hepatitis C Virus Envelope Glycoprotein Structure and Recognition. Frontiers in Immunology. 9: 1117. PMID 29892287 DOI: 10.3389/Fimmu.2018.01117  0.332
2018 Gowthaman R, Pierce BG. TCRmodel: high resolution modeling of T cell receptors from sequence. Nucleic Acids Research. PMID 29790966 DOI: 10.1093/Nar/Gky432  0.365
2017 Pierce BG, Boucher EN, Piepenbrink KH, Ejemel M, Rapp CA, Thomas WD, Sundberg EJ, Weng Z, Wang Y. Structure-Based Design of Hepatitis C Virus Vaccines that Elicit Neutralizing Antibody Responses to a Conserved Epitope. Journal of Virology. PMID 28794021 DOI: 10.1128/Jvi.01032-17  0.505
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  0.617
2016 Pierce BG, Keck ZY, Lau P, Fauvelle C, Gowthaman R, Baumert TF, Fuerst TR, Mariuzza RA, Foung SK. Global mapping of antibody recognition of the hepatitis C virus E2 glycoprotein: Implications for vaccine design. Proceedings of the National Academy of Sciences of the United States of America. PMID 27791171 DOI: 10.1073/Pnas.1614942113  0.326
2016 Vreven T, Pierce BG, Borrman TM, Weng Z. Performance of ZDOCK and IRAD in CAPRI rounds 28-34. Proteins. PMID 27718275 DOI: 10.1002/Prot.25186  0.644
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  0.559
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Pierce BG, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.652
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  0.588
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  0.589
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  0.553
2015 Yang X, Gao M, Chen G, Pierce BG, Lu J, Weng NP, Mariuzza RA. Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope. The Journal of Biological Chemistry. PMID 26429912 DOI: 10.1074/Jbc.M115.691311  0.321
2015 Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Journal of Molecular Biology. 427: 3031-41. PMID 26231283 DOI: 10.1016/J.Jmb.2015.07.016  0.679
2014 Pierce BG, Vreven T, Weng Z. Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. Bmc Bioinformatics. 15: 319. PMID 25260513 DOI: 10.1186/1471-2105-15-319  0.544
2014 Babcock GJ, Iyer S, Smith HL, Wang Y, Rowley K, Ambrosino DM, Zamore PD, Pierce BG, Molrine DC, Weng Z. High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody. Plos One. 9: e100325. PMID 24956119 DOI: 10.1371/Journal.Pone.0100325  0.471
2014 Trastoy B, Lomino JV, Pierce BG, Carter LG, Günther S, Giddens JP, Snyder GA, Weiss TM, Weng Z, Wang LX, Sundberg EJ. Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies. Proceedings of the National Academy of Sciences of the United States of America. 111: 6714-9. PMID 24753590 DOI: 10.1073/Pnas.1322908111  0.524
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  0.589
2014 Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics (Oxford, England). 30: 1771-3. PMID 24532726 DOI: 10.1093/Bioinformatics/Btu097  0.809
2014 Haidar JN, Zhu W, Lypowy J, Pierce BG, Bari A, Persaud K, Luna X, Snavely M, Ludwig D, Weng Z. Backbone flexibility of CDR3 and immune recognition of antigens. Journal of Molecular Biology. 426: 1583-99. PMID 24380763 DOI: 10.1016/J.Jmb.2013.12.024  0.611
2014 Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, ... ... Pierce BG, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439  0.799
2014 Vreven T, Hwang H, Pierce BG, Weng Z. Evaluating template-based and template-free protein-protein complex structure prediction. Briefings in Bioinformatics. 15: 169-76. PMID 23818491 DOI: 10.1093/Bib/Bbt047  0.806
2014 Babcock GJ, Iyer S, Smith HL, Wang Y, Rowley K, Ambrosino DM, Zamore PD, Pierce BG, Molrine DC, Weng Z. Changes in viral loads and epitope sequence distributions in placebo subjects. Plos One. DOI: 10.1371/Journal.Pone.0100325.G002  0.447
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  0.507
2013 Vreven T, Pierce BG, Hwang H, Weng Z. Performance of ZDOCK in CAPRI rounds 20-26. Proteins. 81: 2175-82. PMID 24123140 DOI: 10.1002/Prot.24432  0.82
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Pierce BG, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.801
2013 Pierce BG, Eberwine R, Noble JA, Habib M, Shulha HP, Weng Z, Blankenhorn EP, Mordes JP. The Missing Heritability in T1D and Potential New Targets for Prevention. Journal of Diabetes Research. 2013: 737485. PMID 23691517 DOI: 10.1155/2013/737485  0.703
2013 Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Research. 41: D171-6. PMID 23203885 DOI: 10.1093/Nar/Gks1221  0.712
2013 Pierce BG, Weng Z. A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes. Protein Science : a Publication of the Protein Society. 22: 35-46. PMID 23109003 DOI: 10.1002/Pro.2181  0.675
2012 Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Research. 22: 1798-812. PMID 22955990 DOI: 10.1101/Gr.139105.112  0.732
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  0.544
2012 Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA. Exploring the DNA-recognition potential of homeodomains. Genome Research. 22: 1889-98. PMID 22539651 DOI: 10.1101/Gr.139014.112  0.516
2012 Vreven T, Hwang H, Pierce BG, Weng Z. Prediction of protein-protein binding free energies. Protein Science : a Publication of the Protein Society. 21: 396-404. PMID 22238219 DOI: 10.1002/Pro.2027  0.809
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Pierce BG, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031  0.799
2011 Pierce BG, Hourai Y, Weng Z. Accelerating protein docking in ZDOCK using an advanced 3D convolution library. Plos One. 6: e24657. PMID 21949741 DOI: 10.1371/Journal.Pone.0024657  0.624
2011 Bonsor DA, Postel S, Pierce BG, Wang N, Zhu P, Buonpane RA, Weng Z, Kranz DM, Sundberg EJ. Molecular basis of a million-fold affinity maturation process in a protein-protein interaction. Journal of Molecular Biology. 411: 321-8. PMID 21689661 DOI: 10.1016/J.Jmb.2011.06.009  0.619
2010 Hwang H, Vreven T, Pierce BG, Hung JH, Weng Z. Performance of ZDOCK and ZRANK in CAPRI rounds 13-19 Proteins: Structure, Function and Bioinformatics. 78: 3104-3110. PMID 20936681 DOI: 10.1002/Prot.22764  0.799
2010 Pierce BG, Haidar JN, Yu Y, Weng Z. Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains. Biochemistry. 49: 7050-9. PMID 20681514 DOI: 10.1021/Bi901969A  0.556
2010 Han SJ, Hu J, Pierce B, Weng Z, Renne R. Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins. The Journal of General Virology. 91: 2203-15. PMID 20484563 DOI: 10.1099/Vir.0.020958-0  0.565
2009 Haidar JN, Pierce B, Yu Y, Tong W, Li M, Weng Z. Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC. Proteins. 74: 948-60. PMID 18767161 DOI: 10.1002/Prot.22203  0.783
2008 Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins. 73: 705-9. PMID 18491384 DOI: 10.1002/Prot.22106  0.784
2008 Pierce B, Weng Z. A combination of rescoring and refinement significantly improves protein docking performance. Proteins. 72: 270-9. PMID 18214977 DOI: 10.1002/Prot.21920  0.677
2008 Bastas G, Sompuram SR, Pierce B, Vani K, Bogen SA. Bioinformatic requirements for protein database searching using predicted epitopes from disease-associated antibodies. Molecular & Cellular Proteomics : McP. 7: 247-56. PMID 17897933 DOI: 10.1074/Mcp.M700107-Mcp200  0.462
2007 Wiehe K, Peterson MW, Pierce B, Mintseris J, Weng Z. Protein-protein docking: Overview and performance analysis Methods in Molecular Biology. 413: 283-314. PMID 18075170 DOI: 10.1007/978-1-59745-574-9_11  0.822
2007 Wiehe K, Pierce B, Tong WW, Hwang H, Mintseris J, Weng Z. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins. 69: 719-25. PMID 17803212 DOI: 10.1002/Prot.21747  0.788
2007 Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins. 69: 511-20. PMID 17623839 DOI: 10.1002/Prot.21502  0.815
2007 Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins. 67: 1078-86. PMID 17373710 DOI: 10.1002/Prot.21373  0.608
2005 Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-Protein Docking Benchmark 2.0: an update. Proteins. 60: 214-6. PMID 15981264 DOI: 10.1002/Prot.20560  0.803
2005 Wiehe K, Pierce B, Mintseris J, Tong WW, Anderson R, Chen R, Weng Z. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins. 60: 207-13. PMID 15981263 DOI: 10.1002/Prot.20559  0.799
2005 Pierce B, Tong W, Weng Z. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. Bioinformatics (Oxford, England). 21: 1472-8. PMID 15613396 DOI: 10.1093/Bioinformatics/Bti229  0.776
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