Search Results - "Haddox, Hugh K"

Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture by Haddox, Hugh K, Dingens, Adam S, Bloom, Jesse D

“…HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid sequence evolution. Knowledge of the functional effects of mutations to…”
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Comprehensive Mapping of HIV-1 Escape from a Broadly Neutralizing Antibody by Dingens, Adam S., Haddox, Hugh K., Overbaugh, Julie, Bloom, Jesse D.

“…Precisely defining how viral mutations affect HIV’s sensitivity to antibodies is vital to develop and evaluate vaccines and antibody immunotherapeutics…”
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Mapping mutational effects along the evolutionary landscape of HIV envelope by Haddox, Hugh K, Dingens, Adam S, Hilton, Sarah K, Overbaugh, Julie, Bloom, Jesse D

“…The immediate evolutionary space accessible to HIV is largely determined by how single amino acid mutations affect fitness. These mutational effects can shift…”
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De novo design of immunoglobulin-like domains by Chidyausiku, Tamuka M., Mendes, Soraia R., Klima, Jason C., Nadal, Marta, Eckhard, Ulrich, Roel-Touris, Jorge, Houliston, Scott, Guevara, Tibisay, Haddox, Hugh K., Moyer, Adam, Arrowsmith, Cheryl H., Gomis-Rüth, F. Xavier, Baker, David, Marcos, Enrique

“…Antibodies, and antibody derivatives such as nanobodies, contain immunoglobulin-like (Ig) β-sandwich scaffolds which anchor the hypervariable antigen-binding…”
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Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV by Dingens, Adam S, Acharya, Priyamvada, Haddox, Hugh K, Rawi, Reda, Xu, Kai, Chuang, Gwo-Yu, Wei, Hui, Zhang, Baoshan, Mascola, John R, Carragher, Bridget, Potter, Clinton S, Overbaugh, Julie, Kwong, Peter D, Bloom, Jesse D

“…Eliciting broadly neutralizing antibodies (bnAbs) targeting envelope (Env) is a major goal of HIV vaccine development, but cross-clade breadth from…”
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Large-scale design and refinement of stable proteins using sequence-only models by Singer, Jedediah M, Novotney, Scott, Strickland, Devin, Haddox, Hugh K, Leiby, Nicholas, Rocklin, Gabriel J, Chow, Cameron M, Roy, Anindya, Bera, Asim K, Motta, Francis C, Cao, Longxing, Strauch, Eva-Maria, Chidyausiku, Tamuka M, Ford, Alex, Ho, Ethan, Zaitzeff, Alexander, Mackenzie, Craig O, Eramian, Hamed, DiMaio, Frank, Grigoryan, Gevorg, Vaughn, Matthew, Stewart, Lance J, Baker, David, Klavins, Eric

“…Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare…”
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Perturbing the energy landscape for improved packing during computational protein design by Maguire, Jack B., Haddox, Hugh K., Strickland, Devin, Halabiya, Samer F., Coventry, Brian, Griffin, Jermel R., Pulavarti, Surya V. S. R. K, Cummins, Matthew, Thieker, David F, Klavins, Eric, Szyperski, Thomas, DiMaio, Frank, Baker, David, Kuhlman, Brian

“…The FastDesign protocol in the molecular modeling program Rosetta iterates between sequence optimization and structure refinement to stabilize de novo designed…”
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De novo design of obligate ABC-type heterotrimeric proteins by Bermeo, Sherry, Favor, Andrew, Chang, Ya-Ting, Norris, Andrew, Boyken, Scott E., Hsia, Yang, Haddox, Hugh K., Xu, Chunfu, Brunette, T. J., Wysocki, Vicki H., Bhabha, Gira, Ekiert, Damian C., Baker, David

“…The de novo design of three protein chains that associate to form a heterotrimer (but not any of the possible two-chain heterodimers) and that can drive the…”
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Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex by Carr, Caleb R, Crawford, Katharine H D, Murphy, Michael, Galloway, Jared G, Haddox, Hugh K, Matsen, 4th, Frederick A, Andersen, Kristian G, King, Neil P, Bloom, Jesse D

“…Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host, Mastomys rodents. Efforts to create…”
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Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation by Kim, Tae-Eun, Tsuboyama, Kotaro, Houliston, Scott, Martell, Cydney M, Phoumyvong, Claire M, Lemak, Alexander, Haddox, Hugh K, Arrowsmith, Cheryl H, Rocklin, Gabriel J

“…Designing entirely new protein structures remains challenging because we do not fully understand the biophysical determinants of folding stability. Yet, some…”
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Deep mutational scanning of CYP2C19 in human cells reveals a substrate specificity-abundance tradeoff by Boyle, Gabriel E, Sitko, Katherine, Galloway, Jared G, Haddox, Hugh K, Bianchi, Aisha Haley, Dixon, Ajeya, Wheelock, Melinda K, Vandi, Allyssa J, Wang, Ziyu R, Thomson, Raine E S, Garge, Riddhiman K, Rettie, Allan E, Rubin, Alan F, Geck, Renee C, Gillam, Elizabeth M J, DeWitt, William S, Matsen, 4th, Frederick A, Fowler, Douglas M

“…The Cytochrome P450s (CYPs) enzyme family metabolizes ∼80% of small molecule drugs. Variants in CYPs can substantially alter drug metabolism, leading to…”
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The Role of Configurational Entropy in Miniprotein Stability by Estrada Pabón, Jan D, Haddox, Hugh K, Van Aken, Greg, Pendleton, Ian M, Eramian, Hamed, Singer, Jedediah M, Schrier, Joshua

“…Predicting protein stability is a challenge due to the many competing thermodynamic effects. Through de novo protein design, one begins with a target structure…”
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Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin by Welsh, Frances C, Eguia, Rachel T, Lee, Juhye M, Haddox, Hugh K, Galloway, Jared, Van Vinh Chau, Nguyen, Loes, Andrea N, Huddleston, John, Yu, Timothy C, Quynh Le, Mai, Nhat, Nguyen T D, Thi Le Thanh, Nguyen, Greninger, Alexander L, Chu, Helen Y, Englund, Janet A, Bedford, Trevor, Matsen, 4th, Frederick A, Boni, Maciej F, Bloom, Jesse D

“…Human influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral…”
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Large-scale design and refinement of stable proteins using sequence-only models by Jedediah M Singer, Scott Novotney, Devin Strickland, Hugh K Haddox, Nicholas Leiby, Gabriel J Rocklin, Cameron M Chow, Anindya Roy, Asim K Bera, Francis C Motta, Longxing Cao, Eva-Maria Strauch, Tamuka M Chidyausiku, Alex Ford, Ethan Ho, Alexander Zaitzeff, Craig O Mackenzie, Hamed Eramian, Frank DiMaio, Gevorg Grigoryan, Matthew Vaughn, Lance J Stewart, David Baker, Eric Klavins

“…Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare…”
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