Search Results - "Fleishman, Sarel J"

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability by Goldenzweig, Adi, Goldsmith, Moshe, Hill, Shannon E., Gertman, Or, Laurino, Paola, Ashani, Yacov, Dym, Orly, Unger, Tamar, Albeck, Shira, Prilusky, Jaime, Lieberman, Raquel L., Aharoni, Amir, Silman, Israel, Sussman, Joel L., Tawfik, Dan S., Fleishman, Sarel J.

“…Upon heterologous overexpression, many proteins misfold or aggregate, thus resulting in low functional yields. Human acetylcholinesterase (hAChE), an enzyme…”
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Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution by Fleishman, Sarel J., Baker, David

“…The folding of natural biopolymers into unique three-dimensional structures that determine their function is remarkable considering the vast number of…”
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Practically useful protein-design methods combining phylogenetic and atomistic calculations by Weinstein, Jonathan, Khersonsky, Olga, Fleishman, Sarel J

“…•Stability-threshold effects and biomolecular epistasis limit protein design.•A deeper understanding of these limitations led to successful design methods.•New…”
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Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces by Warszawski, Shira, Borenstein Katz, Aliza, Lipsh, Rosalie, Khmelnitsky, Lev, Ben Nissan, Gili, Javitt, Gabriel, Dym, Orly, Unger, Tamar, Knop, Orli, Albeck, Shira, Diskin, Ron, Fass, Deborah, Sharon, Michal, Fleishman, Sarel J

“…Antibodies developed for research and clinical applications may exhibit suboptimal stability, expressibility, or affinity. Existing optimization strategies…”
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Automated Design of Efficient and Functionally Diverse Enzyme Repertoires by Khersonsky, Olga, Lipsh, Rosalie, Avizemer, Ziv, Ashani, Yacov, Goldsmith, Moshe, Leader, Haim, Dym, Orly, Rogotner, Shelly, Trudeau, Devin L., Prilusky, Jaime, Amengual-Rigo, Pep, Guallar, Victor, Tawfik, Dan S., Fleishman, Sarel J.

“…Substantial improvements in enzyme activity demand multiple mutations at spatially proximal positions in the active site. Such mutations, however, often…”
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Structure and receptor recognition by the Lassa virus spike complex by Katz, Michael, Weinstein, Jonathan, Eilon-Ashkenazy, Maayan, Gehring, Katrin, Cohen-Dvashi, Hadas, Elad, Nadav, Fleishman, Sarel J., Diskin, Ron

“…Lassa virus (LASV) is a human pathogen, causing substantial morbidity and mortality 1 , 2 . Similar to other Arenaviridae , it presents a class-I spike complex…”
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RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite by Fleishman, Sarel J, Leaver-Fay, Andrew, Corn, Jacob E, Strauch, Eva-Maria, Khare, Sagar D, Koga, Nobuyasu, Ashworth, Justin, Murphy, Paul, Richter, Florian, Lemmon, Gordon, Meiler, Jens, Baker, David

“…Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling…”
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Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin by Fleishman, Sarel J., Whitehead, Timothy A., Ekiert, Damian C., Dreyfus, Cyrille, Corn, Jacob E., Strauch, Eva-Maria, Wilson, Ian A., Baker, David

“…We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions…”
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Computational design and molecular dynamics simulations suggest the mode of substrate binding in ceramide synthases by Zelnik, Iris D., Mestre, Beatriz, Weinstein, Jonathan J., Dingjan, Tamir, Izrailov, Stav, Ben-Dor, Shifra, Fleishman, Sarel J., Futerman, Anthony H.

“…Until now, membrane-protein stabilization has relied on iterations of mutations and screening. We now validate a one-step algorithm, mPROSS, for stabilizing…”
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High-resolution mapping of protein sequence-function relationships by Fields, Stanley, Fowler, Douglas M, Araya, Carlos L, Fleishman, Sarel J, Kellogg, Elizabeth H, Stephany, Jason J, Baker, David

“…The combination of protein display, moderate selection for protein activity and high-throughput DNA sequencing can be applied to hundreds of thousands of…”
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Ultrahigh specificity in a network of computationally designed protein-interaction pairs by Netzer, Ravit, Listov, Dina, Lipsh, Rosalie, Dym, Orly, Albeck, Shira, Knop, Orli, Kleanthous, Colin, Fleishman, Sarel J.

“…Protein networks in all organisms comprise homologous interacting pairs. In these networks, some proteins are specific, interacting with one or a few binding…”
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Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing by Whitehead, Timothy A, Chevalier, Aaron, Song, Yifan, Dreyfus, Cyrille, Fleishman, Sarel J, De Mattos, Cecilia, Myers, Chris A, Kamisetty, Hetunandan, Blair, Patrick, Wilson, Ian A, Baker, David

“…To increase the affinity of designed protein inhibitors for influenza hemagglutinin, Whitehead et al . use yeast display and deep sequencing to measure the…”
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Highly active enzymes by automated combinatorial backbone assembly and sequence design by Lapidoth, Gideon, Khersonsky, Olga, Lipsh, Rosalie, Dym, Orly, Albeck, Shira, Rogotner, Shelly, Fleishman, Sarel J.

“…Automated design of enzymes with wild-type-like catalytic properties has been a long-standing but elusive goal. Here, we present a general, automated method…”
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Computational design of a pH-sensitive IgG binding protein by Strauch, Eva-Maria, Fleishman, Sarel J., Baker, David

“…Computational design provides the opportunity to program protein–protein interactions for desired applications. We used de novo protein interface design to…”
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One-step design of a stable variant of the malaria invasion protein RH5 for use as a vaccine immunogen by Campeotto, Ivan, Goldenzweig, Adi, Davey, Jack, Barfod, Lea, Marshall, Jennifer M., Silk, Sarah E., Wright, Katherine E., Draper, Simon J., Higgins, Matthew K., Fleishman, Sarel J.

“…Many promising vaccine candidates from pathogenic viruses, bacteria, and parasites are unstable and cannot be produced cheaply for clinical use. For instance,…”
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Allosteric regulation of the 20S proteasome by the Catalytic Core Regulators (CCRs) family by Deshmukh, Fanindra Kumar, Ben-Nissan, Gili, Olshina, Maya A., Füzesi-Levi, Maria G., Polkinghorn, Caley, Arkind, Galina, Leushkin, Yegor, Fainer, Irit, Fleishman, Sarel J., Tawfik, Dan, Sharon, Michal

“…Controlled degradation of proteins is necessary for ensuring their abundance and sustaining a healthy and accurately functioning proteome. One of the…”
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Designed active-site library reveals thousands of functional GFP variants by Weinstein, Jonathan Yaacov, Martí-Gómez, Carlos, Lipsh-Sokolik, Rosalie, Hoch, Shlomo Yakir, Liebermann, Demian, Nevo, Reinat, Weissman, Haim, Petrovich-Kopitman, Ekaterina, Margulies, David, Ivankov, Dmitry, McCandlish, David M., Fleishman, Sarel J.

“…Mutations in a protein active site can lead to dramatic and useful changes in protein activity. The active site, however, is sensitive to mutations due to a…”
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Emerging themes in the computational design of novel enzymes and protein–protein interfaces by Khare, Sagar D., Fleishman, Sarel J.

“…Recent years have seen the first applications of computational protein design to generate novel catalysts, binding pairs of proteins, protein inhibitors, and…”
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Design of a stable human acid‐β‐glucosidase: towards improved Gaucher disease therapy and mutation classification by Pokorna, Sarka, Khersonsky, Olga, Lipsh‐Sokolik, Rosalie, Goldenzweig, Adi, Nielsen, Rebekka, Ashani, Yacov, Peleg, Yoav, Unger, Tamar, Albeck, Shira, Dym, Orly, Tirosh, Asa, Tarayra, Rana, Hocquemiller, Michaël, Laufer, Ralph, Ben‐Dor, Shifra, Silman, Israel, Sussman, Joel L., Fleishman, Sarel J., Futerman, Anthony H.

“…Acid‐β‐glucosidase (GCase, EC3.2.1.45), the lysosomal enzyme which hydrolyzes the simple glycosphingolipid, glucosylceramide (GlcCer), is encoded by the GBA1…”
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AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences by Lapidoth, Gideon D., Baran, Dror, Pszolla, Gabriele M., Norn, Christoffer, Alon, Assaf, Tyka, Michael D., Fleishman, Sarel J.

“…ABSTRACT Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously…”
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