Publications

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Computational design of the affinity and specificity of a therapeutic T cell receptor.
Pierce BG, Hellman LM, Hossain M, Singh NK, Vander Kooi CW, Weng Z, Baker BM. 2014. Computational design of the affinity and specificity of a therapeutic T cell receptor. PLoS computational biology 10(2): e1003478. DOI: 10.1371/journal.pcbi.1003478
A DNA mimic: the structure and mechanism of action for the anti-repressor protein AbbA.
Tucker AT, Bobay BG, Banse AV, Olson AL, Soderblom EJ, Moseley MA, Thompson RJ, Varney KM, Losick R, Cavanagh J. 2014. A DNA mimic: the structure and mechanism of action for the anti-repressor protein AbbA. Journal of molecular biology 426(9): 1911-24. DOI: 10.1016/j.jmb.2014.02.010
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers.
Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z. 2014. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics (Oxford, England) 30(12): 1771-3. DOI: 10.1093/bioinformatics/btu097
Molecular modeling of nucleic acid structure.
Galindo-Murillo R, Bergonzo C, Cheatham TE. 2013. Molecular modeling of nucleic acid structure. Current protocols in nucleic acid chemistry 54: 7.5.1-7.5.13. DOI: 10.1002/0471142700.nc0705s54
Molecular modeling of nucleic acid structure: energy and sampling.
Bergonzo C, Galindo-Murillo R, Cheatham TE. 2013. Molecular modeling of nucleic acid structure: energy and sampling. Current protocols in nucleic acid chemistry 54: 7.8.1-7.8.21. DOI: 10.1002/0471142700.nc0708s54
First MNKs degrading agents block phosphorylation of eIF4E, induce apoptosis, inhibit cell growth, migration and invasion in triple negative and Her2-overexpressing breast cancer cell lines.
Ramalingam S, Gediya L, Kwegyir-Afful AK, Ramamurthy VP, Purushottamachar P, Mbatia H, Njar VC. 2014. First MNKs degrading agents block phosphorylation of eIF4E, induce apoptosis, inhibit cell growth, migration and invasion in triple negative and Her2-overexpressing breast cancer cell lines. Oncotarget 5(2): 530-43.
Proof of principle for epitope-focused vaccine design.
Correia BE, Bates JT, Loomis RJ, Baneyx G, Carrico C, Jardine JG, Rupert P, Correnti C, Kalyuzhniy O, Vittal V, et al. 2014. Proof of principle for epitope-focused vaccine design. Nature 507(7491): 201-6. DOI: 10.1038/nature12966
Compartmentalized multilayer hydrogel formation using a stimulus-responsive self-assembling polysaccharide.
Xiong Y, Yan K, Bentley WE, Deng H, Du Y, Payne GF, Shi XW. 2014. Compartmentalized multilayer hydrogel formation using a stimulus-responsive self-assembling polysaccharide. ACS applied materials & interfaces 6(4): 2948-57. DOI: 10.1021/am405544r
Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide.
Bergonzo C, Henriksen NM, Roe DR, Swails JM, Roitberg AE, Cheatham TE. 2014. Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide. Journal of chemical theory and computation 10(1): 492-499.
Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment.
Liu Y, Prigozhin MB, Schulten K, Gruebele M. 2014. Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment. Journal of the American Chemical Society 136(11): 4265-72. DOI: 10.1021/ja412639u
Antibodies VRC01 and 10E8 neutralize HIV-1 with high breadth and potency even with Ig-framework regions substantially reverted to germline.
Georgiev IS, Rudicell RS, Saunders KO, Shi W, Kirys T, McKee K, O'Dell S, Chuang GY, Yang ZY, Ofek G, et al. 2014. Antibodies VRC01 and 10E8 neutralize HIV-1 with high breadth and potency even with Ig-framework regions substantially reverted to germline. Journal of immunology (Baltimore, Md. : 1950) 192(3): 1100-1106. DOI: 10.4049/jimmunol.1302515
Backbone flexibility of CDR3 and immune recognition of antigens.
Haidar JN, Zhu W, Lypowy J, Pierce BG, Bari A, Persaud K, Luna X, Snavely M, Ludwig D, Weng Z. 2014. Backbone flexibility of CDR3 and immune recognition of antigens. Journal of molecular biology 426(7): 1583-99. DOI: 10.1016/j.jmb.2013.12.024
A positive cooperativity binding model between Ly49 natural killer cell receptors and the viral immunoevasin m157: kinetic and thermodynamic studies.
Romasanta PN, Curto LM, Urtasun N, Sarratea MB, Chiappini S, Miranda MV, Delfino JM, Mariuzza RA, Fernández MM, Malchiodi EL. 2014. A positive cooperativity binding model between Ly49 natural killer cell receptors and the viral immunoevasin m157: kinetic and thermodynamic studies. The Journal of biological chemistry 289(8): 5083-96. DOI: 10.1074/jbc.M113.532929
Small G proteins Rac1 and Ras regulate serine/threonine protein phosphatase 5 (PP5)·extracellular signal-regulated kinase (ERK) complexes involved in the feedback regulation of Raf1.
Mazalouskas MD, Godoy-Ruiz R, Weber DJ, Zimmer DB, Honkanen RE, Wadzinski BE. 2014. Small G proteins Rac1 and Ras regulate serine/threonine protein phosphatase 5 (PP5)·extracellular signal-regulated kinase (ERK) complexes involved in the feedback regulation of Raf1. The Journal of biological chemistry 289(7): 4219-32. DOI: 10.1074/jbc.M113.518514
Reconstitution of cholesterol-dependent vaginolysin into tethered phospholipid bilayers: implications for bioanalysis.
Budvytyte R, Pleckaityte M, Zvirbliene A, Vanderah DJ, Valincius G. 2013. Reconstitution of cholesterol-dependent vaginolysin into tethered phospholipid bilayers: implications for bioanalysis. PloS one 8(12): e82536. DOI: 10.1371/journal.pone.0082536