Search Results - "Donald, Bruce R"

Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env by Do Kwon, Young, Pancera, Marie, Acharya, Priyamvada, Georgiev, Ivelin S, Crooks, Emma T, Gorman, Jason, Joyce, M Gordon, Guttman, Miklos, Ma, Xiaochu, Narpala, Sandeep, Soto, Cinque, Terry, Daniel S, Yang, Yongping, Zhou, Tongqing, Ahlsen, Goran, Bailer, Robert T, Chambers, Michael, Chuang, Gwo-Yu, Doria-Rose, Nicole A, Druz, Aliaksandr, Hallen, Mark A, Harned, Adam, Kirys, Tatsiana, Louder, Mark K, O'Dell, Sijy, Ofek, Gilad, Osawa, Keiko, Prabhakaran, Madhu, Sastry, Mallika, Stewart-Jones, Guillaume B E, Stuckey, Jonathan, Thomas, Paul V, Tittley, Tishina, Williams, Constance, Zhang, Baoshan, Zhao, Hong, Zhou, Zhou, Donald, Bruce R, Lee, Lawrence K, Zolla-Pazner, Susan, Baxa, Ulrich, Schön, Arne, Freire, Ernesto, Shapiro, Lawrence, Lee, Kelly K, Arthos, James, Munro, James B, Blanchard, Scott C, Mothes, Walther, Binley, James M, McDermott, Adrian B, Mascola, John R, Kwong, Peter D

“…The structure of the ligand-free HIV-1–Env trimer allows conformational fixation of Env and generation of an antigen that binds CD4 with high affinity and is…”
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Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus by Wang, Siyu, Reeve, Stephanie M, Holt, Graham T, Ojewole, Adegoke A, Frenkel, Marcel S, Gainza, Pablo, Keshipeddy, Santosh, Fowler, Vance G, Wright, Dennis L, Donald, Bruce R

“…Antimicrobial resistance presents a significant health care crisis. The mutation F98Y in Staphylococcus aureus dihydrofolate reductase (SaDHFR) confers…”
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Protein design using continuous rotamers by Gainza, Pablo, Roberts, Kyle E, Donald, Bruce R

“…Optimizing amino acid conformation and identity is a central problem in computational protein design. Protein design algorithms must allow realistic protein…”
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Computational Structure-Based Redesign of Enzyme Activity by Chen, Cheng-Yu, Georgiev, Ivelin, Anderson, Amy C., Donald, Bruce R., Richardson, Jane S.

“…We report a computational, structure-based redesign of the phenylalanine adenylation domain of the nonribosomal peptide synthetase enzyme gramicidin S…”
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Planning and control for microassembly of structures composed of stress-engineered MEMS microrobots by Donald, Bruce R, Levey, Christopher G, Paprotny, Igor, Rus, Daniela

“…We present control strategies that implement planar microassembly using groups of stress-engineered MEMS microrobots (MicroStressBots) controlled through a…”
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Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface by Lowegard, Anna U, Frenkel, Marcel S, Holt, Graham T, Jou, Jonathan D, Ojewole, Adegoke A, Donald, Bruce R

“…The K* algorithm provably approximates partition functions for a set of states (e.g., protein, ligand, and protein-ligand complex) to a user-specified accuracy…”
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Computational design of a PDZ domain peptide inhibitor that rescues CFTR activity by Roberts, Kyle E, Cushing, Patrick R, Boisguerin, Prisca, Madden, Dean R, Donald, Bruce R

“…The cystic fibrosis transmembrane conductance regulator (CFTR) is an epithelial chloride channel mutated in patients with cystic fibrosis (CF). The most…”
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Intracellular Neural Recording with Pure Carbon Nanotube Probes by Yoon, Inho, Hamaguchi, Kosuke, Borzenets, Ivan V, Finkelstein, Gleb, Mooney, Richard, Donald, Bruce R

“…The computational complexity of the brain depends in part on a neuron's capacity to integrate electrochemical information from vast numbers of synaptic inputs…”
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Protocol for predicting drug-resistant protein mutations to an ERK2 inhibitor using RESISTOR by Guerin, Nathan, Kaserer, Teresa, Donald, Bruce R.

“…Prospective predictions of drug-resistant protein mutants could improve the design of therapeutics less prone to resistance. Here, we describe RESISTOR, an…”
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Predicting resistance mutations using protein design algorithms by Frey, Kathleen M., Georgiev, Ivelin, Donald, Bruce R., Anderson, Amy C., Stroud, Robert M.

“…Drug resistance resulting from mutations to the target is an unfortunate common phenomenon that limits the lifetime of many of the most successful drugs. In…”
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Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design by Holt, Graham T., Gorman, Jason, Wang, Siyu, Lowegard, Anna U., Zhang, Baoshan, Liu, Tracy, Lin, Bob C., Louder, Mark K., Frenkel, Marcel S., McKee, Krisha, O’Dell, Sijy, Rawi, Reda, Shen, Chen-Hsiang, Doria-Rose, Nicole A., Kwong, Peter D., Donald, Bruce R.

“…Broadly neutralizing antibodies (bNAbs) against HIV can reduce viral transmission in humans, but an effective therapeutic will require unusually high breadth…”
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Discovery, characterization, and redesign of potent antimicrobial thanatin orthologs from Chinavia ubica and Murgantia histrionica targeting E. coli LptA by Huynh, Kelly, Kibrom, Amanuel, Donald, Bruce R., Zhou, Pei

“…[Display omitted] Podisus maculiventris thanatin has been reported as a potent antimicrobial peptide with antibacterial and antifungal activity. Its antibiotic…”
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Protein design algorithms predict viable resistance to an experimental antifolate by Reeve, Stephanie M., Gainza, Pablo, Frey, Kathleen M., Georgiev, Ivelin, Donald, Bruce R., Anderson, Amy C.

“…Significance Computationally predicting drug resistance mutations early in the discovery phase would be an important breakthrough in drug development. The most…”
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Fast search algorithms for computational protein design by Traoré, Seydou, Roberts, Kyle E., Allouche, David, Donald, Bruce R., André, Isabelle, Schiex, Thomas, Barbe, Sophie

“…One of the main challenges in computational protein design (CPD) is the huge size of the protein sequence and conformational space that has to be…”
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Structure of an HIV-1–neutralizing antibody target, the lipid-bound gp41 envelope membrane proximal region trimer by Reardon, Patrick N., Sage, Harvey, Dennison, S. Moses, Martin, Jeffrey W., Donald, Bruce R., Alam, S. Munir, Haynes, Barton F., Spicer, Leonard D.

“…The membrane proximal external region (MPER) of HIV-1 glycoprotein (gp) 41 is involved in viral–host cell membrane fusion. It contains short amino acid…”
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Auditory synapses to song premotor neurons are gated off during vocalization in zebra finches by Hamaguchi, Kosuke, Tschida, Katherine A, Yoon, Inho, Donald, Bruce R, Mooney, Richard

“…Songbirds use auditory feedback to learn and maintain their songs, but how feedback interacts with vocal motor circuitry remains unclear. A potential site for…”
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Disruptor: Computational identification of oncogenic mutants disrupting protein-protein and protein-DNA interactions by Kugler, Valentina, Lieb, Andreas, Guerin, Nathan, Donald, Bruce R., Stefan, Eduard, Kaserer, Teresa

“…We report an Osprey-based computational protocol to prospectively identify oncogenic mutations that act via disruption of molecular interactions. It is…”
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A critical analysis of computational protein design with sparse residue interaction graphs by Jain, Swati, Jou, Jonathan D, Georgiev, Ivelin S, Donald, Bruce R

“…Protein design algorithms enumerate a combinatorial number of candidate structures to compute the Global Minimum Energy Conformation (GMEC). To efficiently…”
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The role of local backrub motions in evolved and designed mutations by Keedy, Daniel A, Georgiev, Ivelin, Triplett, Edward B, Donald, Bruce R, Richardson, David C, Richardson, Jane S

“…Amino acid substitutions in protein structures often require subtle backbone adjustments that are difficult to model in atomic detail. An improved ability to…”
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RESISTOR: A New OSPREY Module to Predict Resistance Mutations by Guerin, Nathan, Kaserer, Teresa, Donald, Bruce R

“…Computational, in silico prediction of resistance-conferring escape mutations could accelerate the design of therapeutics less prone to resistance. This…”
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