Search Results - "Novak, Walter R"

Investigating evolutionary relationships through cluster analysis: A teaching science with big data workshop session by Novak, Walter R.P.

“…Biochemistry is a data‐heavy discipline, yet teaching students to work with large datasets is absent from many undergraduate Biochemistry programs. Ensuring…”
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SARS‐CoV‐2 virtual biochemistry labs on bioinformatics and drug design by Brandt, Gabriel S., Novak, Walter R. P.

“…Colleges and universities are learning to provide relevant virtual lab experiences for students due to the COVID‐19 pandemic. Even schools attempting in‐person…”
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An expanded framework for biomolecular visualization in the classroom: Learning goals and competencies by Dries, Daniel R., Dean, Diane M., Listenberger, Laura L., Novak, Walter R.P., Franzen, Margaret A., Craig, Paul A.

“…A thorough understanding of the molecular biosciences requires the ability to visualize and manipulate molecules in order to interpret results or to generate…”
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Divergence of Function in the Thioredoxin Fold Suprafamily:  Evidence for Evolution of Peroxiredoxins from a Thioredoxin-like Ancestor by Copley, Shelley D, Novak, Walter R. P, Babbitt, Patricia C

“…The thioredoxin fold is found in proteins that serve a wide variety of functions. Among these are peroxiredoxins, which catalyze the reduction of hydrogen…”
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Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida by Brodkin, Heather R, Novak, Walter R. P, Milne, Amy C, D’Aquino, J. Alejandro, Karabacak, N. M, Goldberg, Ilana G, Agar, Jeffrey N, Payne, Mark S, Petsko, Gregory A, Ondrechen, Mary Jo, Ringe, Dagmar

“…Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell…”
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Seeing Eye to Eye? Comparing Faculty and Student Perceptions of Biomolecular Visualization Assessments by Beckham, Josh T., Dries, Daniel R., Hall, Bonnie L., Mitton-Fry, Rachel M., Engelman, Shelly, Burch, Charmita, Acevedo, Roderico, Mertz, Pamela S., Vardar-Ulu, Didem, Agrawal, Swati, Fox, Kristin M., Austin, Shane, Franzen, Margaret A., Jakubowski, Henry V., Novak, Walter R. P., Roberts, Rebecca, Roca, Alberto I., Procko, Kristen

“…While visual literacy has been identified as a foundational skill in life science education, there are many challenges in teaching and assessing biomolecular…”
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Meeting report: BioMolViz workshops for developing assessments of biomolecular visual literacy by Procko, Kristen, Engelman, Shelly, Jakubowski, Henry, Beckham, Josh T., Dean, Diane M., Franzen, Margaret A., Novak, Walter R. P., Roberts, Rebecca, Roca, Alberto I., Shor, Audrey C., Terrell, Cassidy R., Dries, Daniel R.

“…While molecular visualization has been recognized as a threshold concept in biology education, the explicit assessment of students' visual literacy skills is…”
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Enhancing student retention of prerequisite knowledge through pre‐class activities and in‐class reinforcement by Taylor, Ann T.S., Olofson, Eric L., Novak, Walter R.P.

“…To foster the connection between biochemistry and the supporting prerequisite concepts, a collection of activities that explicitly link general and organic…”
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Using a Deliberation of Energy Policy as an Educational Tool in a Nonmajors Chemistry Course by Drury, Sara A. Mehltretter, Stucker, Kyle, Douglas, Anthony, Rush, Ryan A, Novak, Walter R. P, Wysocki, Laura M

“…A central goal of nonmajors chemistry courses is to instill within students the sense that chemistry does not occur in a vacuum but rather permeates everyday…”
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A Bulky Hydrophobic Residue Is Not Required To Maintain the V‑Conformation of Enzyme-Bound Thiamin Diphosphate by Andrews, Forest H, Tom, Alan R, Gunderman, Peter R, Novak, Walter R. P, McLeish, Michael J

“…It is widely accepted that, in thiamin diphosphate (ThDP)-dependent enzymes, much of the rate acceleration is provided by the cofactor. Inter alia, the…”
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De novo design of bioactive protein switches by Langan, Robert A., Boyken, Scott E., Ng, Andrew H., Samson, Jennifer A., Dods, Galen, Westbrook, Alexandra M., Nguyen, Taylor H., Lajoie, Marc J., Chen, Zibo, Berger, Stephanie, Mulligan, Vikram Khipple, Dueber, John E., Novak, Walter R. P., El-Samad, Hana, Baker, David

“…Allosteric regulation of protein function is widespread in biology, but is challenging for de novo protein design as it requires the explicit design of…”
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Sequential unfolding of the hemolysin two‐partner secretion domain from Proteus mirabilis by Wimmer, Megan R., Woods, Christopher N., Adamczak, Kyle J., Glasgow, Evan M., Novak, Walter R.P., Grilley, Daniel P., Weaver, Todd M.

“…Protein secretion is a major contributor to Gram‐negative bacterial virulence. Type Vb or two‐partner secretion (TPS) pathways utilize a membrane bound…”
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d-Ribulose 5-Phosphate 3-Epimerase:  Functional and Structural Relationships to Members of the Ribulose-Phosphate Binding (β/α)8-Barrel Superfamily by Akana, Julie, Fedorov, Alexander A, Fedorov, Elena, Novak, Walter R. P, Babbitt, Patricia C, Almo, Steven C, Gerlt, John A

“…The “ribulose phosphate binding” superfamily defined by the Structural Classification of Proteins (SCOP) database is considered the result of divergent…”
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Optimizing the cODC degron for Protein Control in Nematode Worms by Valero‐Davlia, Felix, Johnson, Grant M., Huynh, Nhan, Sorensen, Erika B., Novak, Walter R.

“…Caenorhabditis elegans, a nematode worm, is a model multicellular organism for the study of development and disease. Current methods of controlling essential…”
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Proteolysis of truncated hemolysin A yields a stable dimerization interface by Novak, Walter R. P., Bhattacharyya, Basudeb, Grilley, Daniel P., Weaver, Todd M.

“…Wild‐type and variant forms of HpmA265 (truncated hemolysin A) from Proteus mirabilis reveal a right‐handed, parallel β‐helix capped and flanked by segments of…”
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Using De Novo Designed Protein Switches in C. elegans by Berg, Adam P., Kaefer, Joseph H., Wakefield, Connor M., Faber, Jakob L., Novak, Walter R., Sorensen, Erika B.

“…The ‘Latching Orthogonal Cage/Key pRoteins’ (LOCKR) system is a de novo designed protein Switch and Key. The Switch functions to cage a functional protein…”
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Developing Assessments to Gauge Biomolecular Visual Literacy: A 5 step approach to ensuring accuracy and reliability by Procko, Kristen, Engelman, Shelly, Beckham, Josh, Dries, Dan R., Franzen, Margaret A., Jakubowski, Henry, Novak, Walter R., Roberts, Rebecca, Roca, Alberto I., Shor, Audrey C.

“…BioMolViz is a community of educators, assessment experts, and biomolecular visualization enthusiasts dedicated to improving biomolecular visual literacy. A…”
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Isoleucine 69 and Valine 325 Form a Specificity Pocket in Human Muscle Creatine Kinase by Novak, Walter R. P, Wang, Pan-Fen, McLeish, Michael J, Kenyon, George L, Babbitt, Patricia C

“…Creatine kinase (CK) catalyzes the reversible phosphorylation of creatine by ATP. From a structural perspective, the enzyme utilizes two flexible loop regions…”
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Modeling an Enzyme Active Site using Molecular Visualization Freeware by Procko, Kristen, Bakheet, Sandy, Beckham, Josh T, Franzen, Margaret A, Jakubowski, Henry, Novak, Walter R P

“…Biomolecular visualization skills are paramount to understanding key concepts in the biological sciences, such as structure-function relationships and…”
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Prediction of distal residue participation in enzyme catalysis by Brodkin, Heather R, DeLateur, Nicholas A, Somarowthu, Srinivas, Mills, Caitlyn L, Novak, Walter R, Beuning, Penny J, Ringe, Dagmar, Ondrechen, Mary Jo

“…A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal…”
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