Search Results - "Chivian, Dylan"

Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases by Ma, Suzanne M., Garcia, David E., Redding-Johanson, Alyssa M., Friedland, Gregory D., Chan, Rossana, Batth, Tanveer S., Haliburton, John R., Chivian, Dylan, Keasling, Jay D., Petzold, Christopher J., Soon Lee, Taek, Chhabra, Swapnil R.

“…Expression of foreign pathways often results in suboptimal performance due to unintended factors such as introduction of toxic metabolites, cofactor imbalances…”
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Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth by Chivian, Dylan, Brodie, Eoin L, Alm, Eric J, Culley, David E, Dehal, Paramvir S, DeSantis, Todd Z, Gihring, Thomas M, Lapidus, Alla, Lin, Li-Hung, Lowry, Stephen R, Moser, Duane P, Richardson, Paul M, Southam, Gordon, Wanger, Greg, Pratt, Lisa M, Andersen, Gary L, Hazen, Terry C, Brockman, Fred J, Arkin, Adam P, Onstott, Tullis C

“…DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete…”
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Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli by McKee, Adrienne E, Rutherford, Becky J, Chivian, Dylan C, Baidoo, Edward K, Juminaga, Darmawi, Kuo, Dwight, Benke, Peter I, Dietrich, Jeffrey A, Ma, Suzanne M, Arkin, Adam P, Petzold, Christopher J, Adams, Paul D, Keasling, Jay D, Chhabra, Swapnil R

“…Microbial engineering strategies that elicit global metabolic perturbations have the capacity to increase organism robustness for targeted metabolite…”
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Changes in microbial dynamics during long-term decomposition in tropical forests by DeAngelis, Kristen M., Chivian, Dylan, Fortney, Julian L., Arkin, Adam P., Simmons, Blake, Hazen, Terry C., Silver, Whendee L.

“…Humid tropical forest soils are characterized by low and fluctuating redox, conditions which are thought to inhibit organic matter degradation by microbes…”
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Phylogenomically Guided Identification of Industrially Relevant GH1 β‑Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry by Heins, Richard A, Cheng, Xiaoliang, Nath, Sangeeta, Deng, Kai, Bowen, Benjamin P, Chivian, Dylan C, Datta, Supratim, Friedland, Gregory D, D’Haeseleer, Patrik, Wu, Dongying, Tran-Gyamfi, Mary, Scullin, Chessa S, Singh, Seema, Shi, Weibing, Hamilton, Matthew G, Bendall, Matthew L, Sczyrba, Alexander, Thompson, John, Feldman, Taya, Guenther, Joel M, Gladden, John M, Cheng, Jan-Fang, Adams, Paul D, Rubin, Edward M, Simmons, Blake A, Sale, Kenneth L, Northen, Trent R, Deutsch, Samuel

“…Harnessing the biotechnological potential of the large number of proteins available in sequence databases requires scalable methods for functional…”
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Physically Realistic Homology Models Built with ROSETTA Can Be More Accurate than Their Templates by Misura, Kira M. S., Chivian, Dylan, Rohl, Carol A., Kim, David E., Baker, David

“…We have developed a method that combines the ROSETTA de novo protein folding and refinement protocol with distance constraints derived from homologous…”
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De Novo Prediction of Three-dimensional Structures for Major Protein Families by Bonneau, Richard, Strauss, Charlie E.M, Rohl, Carol A, Chivian, Dylan, Bradley, Phillip, Malmström, Lars, Robertson, Tim, Baker, David

“…We use the Rosetta de novo structure prediction method to produce three-dimensional structure models for all Pfam-A sequence families with average length under…”
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Tracing Determinants of Dual Substrate Specificity in Glycoside Hydrolase Family 5 by Chen, Zhiwei, Friedland, Gregory D., Pereira, Jose H., Reveco, Sonia A., Chan, Rosa, Park, Joshua I., Thelen, Michael P., Adams, Paul D., Arkin, Adam P., Keasling, Jay D., Blanch, Harvey W., Simmons, Blake A., Sale, Kenneth L., Chivian, Dylan, Chhabra, Swapnil R.

“…Background: Glycoside hydrolase family 5 (GH5) comprises enzymes with a wide range of activities critical for the deconstruction of lignocellulose. Results:…”
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Automated prediction of CASP-5 structures using the Robetta server by Chivian, Dylan, Kim, David E., Malmström, Lars, Bradley, Philip, Robertson, Timothy, Murphy, Paul, Strauss, Charles E.M., Bonneau, Richard, Rohl, Carol A., Baker, David

“…Robetta is a fully automated protein structure prediction server that uses the Rosetta fragment‐insertion method. It combines template‐based and de novo…”
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Prediction of CASP6 structures using automated robetta protocols by Chivian, Dylan, Kim, David E., Malmström, Lars, Schonbrun, Jack, Rohl, Carol A., Baker, David

“…The Robetta server and revised automatic protocols were used to predict structures for CASP6 targets. Robetta is a publicly available protein structure…”
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Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM by Kim, David E., Chivian, Dylan, Malmström, Lars, Baker, David

“…Domain boundary prediction is an important step in both experimental and computational protein structure characterization. We have developed two fully…”
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Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation by Bradley, Philip, Chivian, Dylan, Meiler, Jens, Misura, Kira M.S., Rohl, Carol A., Schief, William R., Wedemeyer, William J., Schueler-Furman, Ora, Murphy, Paul, Schonbrun, Jack, Strauss, Charles E.M., Baker, David

“…We describe predictions of the structures of CASP5 targets using Rosetta. The Rosetta fragment insertion protocol was used to generate models for entire target…”
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Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology by Malmström, Lars, Riffle, Michael, Strauss, Charlie E M, Chivian, Dylan, Davis, Trisha N, Bonneau, Richard, Baker, David

“…Saccharomyces cerevisiae is one of the best-studied model organisms, yet the three-dimensional structure and molecular function of many yeast proteins remain…”
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Assessment of predictions submitted for the CASP7 domain prediction category by Tress, Michael, Cheng, Jianlin, Baldi, Pierre, Joo, Keehyoung, Lee, Jinwoo, Seo, Joo-Hyun, Lee, Jooyoung, Baker, David, Chivian, Dylan, Kim, David, Ezkurdia, Iakes

“…This paper details the assessment process and evaluation results for the Critical Assessment of Protein Structure Prediction (CASP7) domain prediction…”
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Rosetta in CASP4: Progress in ab initio protein structure prediction by Bonneau, Richard, Tsai, Jerry, Ruczinski, Ingo, Chivian, Dylan, Rohl, Carol, Strauss, Charlie E. M., Baker, David

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In Vivo Oligomerization of the F Conjugative Coupling Protein TraD by HAFT, Rembrandt J. F, GACHELET, Eliora G, NGUYEN, Tran, TOUSSAINT, Luttrell, CHIVIAN, Dylan, TRAXLER, Beth

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection by Chivian, Dylan, Baker, David

“…The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of…”
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KBase: The United States Department of Energy Systems Biology Knowledgebase by Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel M D, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong

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Protein structure prediction and analysis using the Robetta server by Kim, David E., Chivian, Dylan, Baker, David

“…The Robetta server (http://robetta.bakerlab.org) provides automated tools for protein structure prediction and analysis. For structure prediction, sequences…”
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Metagenome-assembled genome extraction and analysis from microbiomes using KBase by Chivian, Dylan, Jungbluth, Sean P., Dehal, Paramvir S., Wood-Charlson, Elisha M., Canon, Richard S., Allen, Benjamin H., Clark, Mikayla M., Gu, Tianhao, Land, Miriam L., Price, Gavin A., Riehl, William J., Sneddon, Michael W., Sutormin, Roman, Zhang, Qizhi, Cottingham, Robert W., Henry, Chris S., Arkin, Adam P.

“…Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun…”
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