Search Results - "Bradley, Philip"

Structure-based prediction of T cell receptor:peptide-MHC interactions by Bradley, Philip

“…The regulatory and effector functions of T cells are initiated by the binding of their cell-surface T cell receptor (TCR) to peptides presented by major…”
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TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs by Mayer-Blackwell, Koshlan, Schattgen, Stefan, Cohen-Lavi, Liel, Crawford, Jeremy C, Souquette, Aisha, Gaevert, Jessica A, Hertz, Tomer, Thomas, Paul G, Bradley, Philip, Fiore-Gartland, Andrew

“…T-cell receptors (TCRs) encode clinically valuable information that reflects prior antigen exposure and potential future response. However, despite advances in…”
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Neural network models for sequence-based TCR and HLA association prediction by Liu, Si, Bradley, Philip, Sun, Wei

“…T cells rely on their T cell receptors (TCRs) to discern foreign antigens presented by human leukocyte antigen (HLA) proteins. The TCRs of an individual…”
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Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules by Park, Hahnbeom, Bradley, Philip, Greisen, Per, Liu, Yuan, Mulligan, Vikram Khipple, Kim, David E, Baker, David, DiMaio, Frank

“…Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking have been parametrized using existing…”
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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design by Alford, Rebecca F, Leaver-Fay, Andrew, Jeliazkov, Jeliazko R, O’Meara, Matthew J, DiMaio, Frank P, Park, Hahnbeom, Shapovalov, Maxim V, Renfrew, P. Douglas, Mulligan, Vikram K, Kappel, Kalli, Labonte, Jason W, Pacella, Michael S, Bonneau, Richard, Bradley, Philip, Dunbrack, Roland L, Das, Rhiju, Baker, David, Kuhlman, Brian, Kortemme, Tanja, Gray, Jeffrey J

“…Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation…”
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U2AF1 mutations alter splice site recognition in hematological malignancies by Ilagan, Janine O, Ramakrishnan, Aravind, Hayes, Brian, Murphy, Michele E, Zebari, Ahmad S, Bradley, Philip, Bradley, Robert K

“…Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological…”
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The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target by Mak, Amanda Nga-Sze, Bradley, Philip, Cernadas, Raul A., Bogdanove, Adam J., Stoddard, Barry L.

“…DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable…”
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Atomistic modeling of protein–DNA interaction specificity: progress and applications by Liu, Limin Angela, Bradley, Philip

“…► We review structure-based approaches for protein–DNA binding specificity prediction. ► Interface flexibility is necessary for accurate template-based…”
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Large-scale characterization of peptide-MHC binding landscapes with structural simulations by Yanover, Chen, Bradley, Philip, Baker, David

“…Class I major histocompatibility complex proteins play a critical role in the adaptive immune system by binding to peptides derived from cytosolic proteins and…”
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Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity by DeWitt, 3rd, William S, Smith, Anajane, Schoch, Gary, Hansen, John A, Matsen, 4th, Frederick A, Bradley, Philip

“…The T cell receptor (TCR) repertoire encodes immune exposure history through the dynamic formation of immunological memory. Statistical analysis of repertoire…”
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Toward High-Resolution de Novo Structure Prediction for Small Proteins by Bradley, Philip, Misura, Kira M. S, Baker, David

“…The prediction of protein structure from amino acid sequence is a grand challenge of computational molecular biology. By using a combination of improved low-…”
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Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets by Crook, Zachary R., Sevilla, Gregory P., Friend, Della, Brusniak, Mi-Youn, Bandaranayake, Ashok D., Clarke, Midori, Gewe, Mesfin, Mhyre, Andrew J., Baker, David, Strong, Roland K., Bradley, Philip, Olson, James M.

“…Protein:protein interactions are among the most difficult to treat molecular mechanisms of disease pathology. Cystine-dense peptides have the potential to…”
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TAL effectors: function, structure, engineering and applications by Mak, Amanda Nga-Sze, Bradley, Philip, Bogdanove, Adam J, Stoddard, Barry L

“…► TAL effectors are highly modular, easily programmable gene targeting proteins. ► Recent crystallographic analyses of TAL effectors have illustrated the basis…”
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Prediction of the Structure of Symmetrical Protein Assemblies by André, Ingemar, Bradley, Philip, Wang, Chu, Baker, David

“…Biological supramolecular systems are commonly built up by the self-assembly of identical protein subunits to produce symmetrical oligomers with cyclical,…”
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High-resolution structure prediction and the crystallographic phase problem by Qian, Bin, Bradley, Philip, Baker, David, McCoy, Airlie J, Read, Randy J, Das, Rhiju, Raman, Srivatsan

“…The energy-based refinement of low-resolution protein structure models to atomic-level accuracy is a major challenge for computational structural biology. Here…”
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De novo design of knotted tandem repeat proteins by Doyle, Lindsey A., Takushi, Brittany, Kibler, Ryan D., Milles, Lukas F., Orozco, Carolina T., Jones, Jonathan D., Jackson, Sophie E., Stoddard, Barry L., Bradley, Philip

“…De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the…”
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A Diverse Lipid Antigen-Specific TCR Repertoire Is Clonally Expanded during Active Tuberculosis by DeWitt, William S, Yu, Krystle K Q, Wilburn, Damien B, Sherwood, Anna, Vignali, Marissa, Day, Cheryl L, Scriba, Thomas J, Robins, Harlan S, Swanson, Willie J, Emerson, Ryan O, Bradley, Philip H, Seshadri, Chetan

“…Human T cells that recognize lipid Ags presented by highly conserved CD1 proteins often express semi-invariant TCRs, but the true diversity of lipid…”
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Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model by Li, Shen, Bradley, Philip

“…When proteins bind to their DNA target sites, ordered water molecules are often present at the protein–DNA interface bridging protein and DNA through hydrogen…”
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Deep generative models for T cell receptor protein sequences by Davidsen, Kristian, Olson, Branden J, DeWitt, 3rd, William S, Feng, Jean, Harkins, Elias, Bradley, Philip, Matsen, 4th, Frederick A

“…Probabilistic models of adaptive immune repertoire sequence distributions can be used to infer the expansion of immune cells in response to stimulus,…”
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Microbiota dictate T cell clonal selection to augment graft-versus-host disease after stem cell transplantation by Yeh, Albert C, Koyama, Motoko, Waltner, Olivia G, Minnie, Simone A, Boiko, Julie R, Shabaneh, Tamer B, Takahashi, Shuichiro, Zhang, Ping, Ensbey, Kathleen S, Schmidt, Christine R, Legg, Samuel R W, Sekiguchi, Tomoko, Nelson, Ethan, Bhise, Shruti S, Stevens, Andrew R, Goodpaster, Tracy, Chakka, Saranya, Furlan, Scott N, Markey, Kate A, Bleakley, Marie E, Elson, Charles O, Bradley, Philip H, Hill, Geoffrey R

“…Allogeneic T cell expansion is the primary determinant of graft-versus-host disease (GVHD), and current dogma dictates that this is driven by…”
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