Search Results - "Alford, Rebecca F"

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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Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane by Alford, Rebecca F., Fleming, Patrick J., Fleming, Karen G., Gray, Jeffrey J.

“…Protein design is a powerful tool for elucidating mechanisms of function and engineering new therapeutics and nanotechnologies. Although soluble protein design…”
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A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design by Alford, Rebecca F, Leaver-Fay, Andrew, Gonzales, Lynda, Dolan, Erin L, Gray, Jeffrey J

“…Computational biology is an interdisciplinary field, and many computational biology research projects involve distributed teams of scientists. To accomplish…”
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An Integrated Framework Advancing Membrane Protein Modeling and Design by Alford, Rebecca F, Koehler Leman, Julia, Weitzner, Brian D, Duran, Amanda M, Tilley, Drew C, Elazar, Assaf, Gray, Jeffrey J

“…Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a…”
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Diverse Scientific Benchmarks for Implicit Membrane Energy Functions by Alford, Rebecca F, Samanta, Rituparna, Gray, Jeffrey J

“…Energy functions are fundamental to biomolecular modeling. Their success depends on robust physical formalisms, efficient optimization, and high-resolution…”
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Membrane Protein Engineering with Rosetta by Alford, Rebecca F, Gray, Jeffrey J

“…Protein engineering can yield new molecular tools for nanotechnology and therapeutic applications through modulating physiochemical and biological properties…”
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Protein docking and steered molecular dynamics suggest alternative phospholamban-binding sites on the SERCA calcium transporter by Alford, Rebecca F., Smolin, Nikolai, Young, Howard S., Gray, Jeffrey J., Robia, Seth L.

“…The transport activity of the sarco(endo)plasmic reticulum calcium ATPase (SERCA) in cardiac myocytes is modulated by an inhibitory interaction with a…”
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Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane by Alford, Rebecca F., Fleming, Patrick J., Fleming, Karen G., Gray, Jeffrey J.

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Robust classification of protein variation using structural modelling and large-scale data integration by Baugh, Evan H, Simmons-Edler, Riley, Müller, Christian L, Alford, Rebecca F, Volfovsky, Natalia, Lash, Alex E, Bonneau, Richard

“…Existing methods for interpreting protein variation focus on annotating mutation pathogenicity rather than detailed interpretation of variant deleteriousness…”
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Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks by Koehler Leman, Julia, Lyskov, Sergey, Lewis, Steven M., Adolf-Bryfogle, Jared, Alford, Rebecca F., Barlow, Kyle, Ben-Aharon, Ziv, Farrell, Daniel, Fell, Jason, Hansen, William A., Harmalkar, Ameya, Jeliazkov, Jeliazko, Kuenze, Georg, Krys, Justyna D., Ljubetič, Ajasja, Loshbaugh, Amanda L., Maguire, Jack, Moretti, Rocco, Mulligan, Vikram Khipple, Nance, Morgan L., Nguyen, Phuong T., Ó Conchúir, Shane, Roy Burman, Shourya S., Samanta, Rituparna, Smith, Shannon T., Teets, Frank, Tiemann, Johanna K. S., Watkins, Andrew, Woods, Hope, Yachnin, Brahm J., Bahl, Christopher D., Bailey-Kellogg, Chris, Baker, David, Das, Rhiju, DiMaio, Frank, Khare, Sagar D., Kortemme, Tanja, Labonte, Jason W., Lindorff-Larsen, Kresten, Meiler, Jens, Schief, William, Schueler-Furman, Ora, Siegel, Justin B., Stein, Amelie, Yarov-Yarovoy, Vladimir, Kuhlman, Brian, Leaver-Fay, Andrew, Gront, Dominik, Gray, Jeffrey J., Bonneau, Richard

“…Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering…”
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A humanized yeast system to analyze cleavage of prelamin A by ZMPSTE24 by Spear, Eric D., Alford, Rebecca F., Babatz, Tim D., Wood, Kaitlin M., Mossberg, Otto W., Odinammadu, Kamsi, Shilagardi, Khurts, Gray, Jeffrey J., Michaelis, Susan

“…•The protease ZMPSTE24 performs the final cleavage step in prelamin A maturation.•Mutations in ZMPSTE24 or LMNA cause progeria and related disorders.•A…”
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Correction to “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.

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Big Data from Sparse Data: Diverse Scientific Benchmarks Reveal Optimization Imperatives for Implicit Membrane Energy Functions by Alford, Rebecca F., Gray, Jeffrey J.

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Toward Accurate Prediction and Design of Kinked Alpha Helices in Membrane Proteins by Lasher, Brittany, Alford, Rebecca F., Gray, Jeffrey J.

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A Thermodynamically-Rigorous, Biologically-Driven Energy Function for Membrane Protein Modeling and Design by Alford, Rebecca F., Fleming, Patrick, Fleming, Karen G., Gray, Jeffrey J.

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Fast Implicit Potentials for Accurate Prediction and Design of Membrane Protein Structures by Alford, Rebecca F., Fleming, Patrick, Fleming, Karen G., Gray, Jeffrey J.

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Rosetta-MPDock: A Novel Computational Tool for Protein-Protein Docking within the Membrane Bilayer by Leman, Julia Koehler, Alford, Rebecca F., Gray, Jeffrey J.

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A Deep-Dive into the Rosetta Energy Function for Biological Macromolecules by Alford, Rebecca F., Leaver-Fay, Andrew, Jeliazkov, Jeliazko R., Pacella, Michael S., Kuhlman, Brian, Kortemme, Tanja, Gray, Jeffrey J.

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Toward Biologically Realistic Computational Membrane Protein Structure Prediction and Design by Alford, Rebecca F

“…Membrane proteins function as gates and checkpoints that control the transit of molecules and information across the lipid bilayer. Understanding their…”
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An Integrated Framework Advancing Membrane Protein Modeling and Design: e1004398 by Alford, Rebecca F, Leman, Julia Koehler, Weitzner, Brian D, Duran, Amanda M, Tilley, Drew C, Elazar, Assaf, Gray, Jeffrey J

“…Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a…”
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