Works by Daggett, Valerie

Results: 68

A CHEMICAL GROUP GRAPH REPRESENTATION FOR EFFICIENT HIGH-THROUGHPUT ANALYSIS OF ATOMISTIC PROTEIN SIMULATIONS.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 4, p. 1250008-1, doi. 10.1142/S0219720012500084

By:

BENSON, NOAH C.;
DAGGETT, VALERIE

Publication type:

Article

The molecular basis of the temperature- and pH-induced conformational transitions in elastin-based peptides.

Published in:

Biopolymers, 2003, v. 68, n. 1, p. 121, doi. 10.1002/bip.10204

By:

Li, Bin;
Daggett, Valerie

Publication type:

Article

Mechanistic insights into the role of amyloid-β in innate immunity.

Published in:

Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-55423-9

By:

Prosswimmer, Tatum;
Heng, Anthony;
Daggett, Valerie

Publication type:

Article

Designed α-sheet peptides disrupt uropathogenic E. coli biofilms rendering bacteria susceptible to antibiotics and immune cells.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-36343-6

By:

Bleem, Alissa;
Prosswimmer, Tatum;
Chen, Ruying;
Hady, Thomas F.;
Li, Jinzheng;
Bryers, James D.;
Daggett, Valerie

Publication type:

Article

Dynameomics: protein dynamics and unfolding across fold space.

Published in:

Biomolecular Concepts, 2010, v. 1, n. 5/6, p. 335, doi. 10.1515/BMC.2010.032

By:

Jonsson, Amanda L.;
Schaeffer, R. Dustin;
van der Kamp, Marc W.;
Daggett, Valerie

Publication type:

Article

Shared unfolding pathways of unrelated immunoglobulin-like β-sandwich proteins.

Published in:

PEDS: Protein Engineering, Design & Selection, 2019, v. 32, n. 7, p. 331, doi. 10.1093/protein/gzz040

By:

Toofanny, Rudesh D;
Calhoun, Sara;
Jonsson, Amanda L;
Daggett, Valerie

Publication type:

Article

Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides.

Published in:

PEDS: Protein Engineering, Design & Selection, 2018, v. 31, n. 6, p. 191, doi. 10.1093/protein/gzy016

By:

Childers, Matthew Carter;
Towse, Clare-Louise;
Daggett, Valerie

Publication type:

Article

An in silico algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein.

Published in:

PEDS: Protein Engineering, Design & Selection, 2016, v. 29, n. 9, p. 377, doi. 10.1093/protein/gzw035

By:

Bromley, Dennis;
Bauer, Matthias R.;
Fersht, Alan R.;
Daggett, Valerie

Publication type:

Article

The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design.

Published in:

PEDS: Protein Engineering, Design & Selection, 2016, v. 29, n. 7, p. 271, doi. 10.1093/protein/gzw023

By:

Childers, Matthew Carter;
Towse, Clare-Louise;
Daggett, Valerie

Publication type:

Article

Nature versus design: the conformational propensities of d-amino acids and the importance of side chain chirality.

Published in:

PEDS: Protein Engineering, Design & Selection, 2014, v. 27, n. 11, p. 447, doi. 10.1093/protein/gzu037

By:

Towse, Clare-Louise;
Hopping, Gene;
Vulovic, Ivan;
Daggett, Valerie

Publication type:

Article

Early steps in thermal unfolding of superoxide dismutase 1 are similar to the conformational changes associated with the ALS-associated A4V mutation.

Published in:

PEDS: Protein Engineering, Design & Selection, 2013, v. 26, n. 8, p. 503, doi. 10.1093/protein/gzt030

By:

Schmidlin, Tom;
Ploeger, Ken;
Jonsson, Amanda L.;
Daggett, Valerie

Publication type:

Article

Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain.

Published in:

PEDS: Protein Engineering, Design & Selection, 2013, v. 26, n. 1, p. 35, doi. 10.1093/protein/gzs063

By:

McCully, Michelle E.;
Beck, David A.C.;
Daggett, Valerie

Publication type:

Article

Disruption of the X-loop turn of the prion protein linked to scrapie resistance.

Published in:

PEDS: Protein Engineering, Design & Selection, 2012, v. 25, n. 5, p. 243, doi. 10.1093/protein/gzs009

By:

Scouras, Alexander D.;
Daggett, Valerie

Publication type:

Article

Protein folds and protein folding.

Published in:

PEDS: Protein Engineering, Design & Selection, 2011, v. 24, n. 1/2, p. 11, doi. 10.1093/protein/gzq096

By:

Schaeffer, R. Dustin;
Daggett, Valerie

Publication type:

Article

Introduction to special issue ‘Three Decades of Protein Engineering: Impact on Structural Biology and Therapy’.

Published in:

PEDS: Protein Engineering, Design & Selection, 2011, v. 24, n. 1/2, p. 1, doi. 10.1093/protein/gzq117

By:

Daggett, Valerie

Publication type:

Article

Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold.

Published in:

PEDS: Protein Engineering, Design & Selection, 2010, v. 23, n. 5, p. 327, doi. 10.1093/protein/gzp090

By:

Merkley, Eric D.;
Parson, William W.;
Daggett, Valerie

Publication type:

Article

The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures.

Published in:

PEDS: Protein Engineering, Design & Selection, 2010, v. 23, n. 1, p. 27, doi. 10.1093/protein/gzp069

By:

Law, Peter B.;
Daggett, Valerie

Publication type:

Article

The V119I polymorphism in protein L-isoaspartate O-methyltransferase alters the substrate-binding interface.

Published in:

PEDS: Protein Engineering, Design & Selection, 2009, v. 22, n. 12, p. 713, doi. 10.1093/protein/gzp056

By:

Rutherford, Karen;
Daggett, Valerie

Publication type:

Article

Shedding light on amyloidosis with protein engineering.

Published in:

PEDS: Protein Engineering, Design & Selection, 2009, v. 22, n. 8, p. 445, doi. 10.1093/protein/gzp049

By:

Daggett, Valerie

Publication type:

Article

The consequences of pathogenic mutations to the human prion protein.

Published in:

PEDS: Protein Engineering, Design & Selection, 2009, v. 22, n. 8, p. 461, doi. 10.1093/protein/gzp039

By:

Van der Kamp, Marc W.;
Daggett, Valerie

Publication type:

Article

Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data.

Published in:

PEDS: Protein Engineering, Design & Selection, 2008, v. 21, n. 6, p. 379, doi. 10.1093/protein/gzn015

By:

Catherine Kehl;
Andrew M. Simms;
Rudesh D. Toofanny;
Valerie Daggett

Publication type:

Article

Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations.

Published in:

PEDS: Protein Engineering, Design & Selection, 2008, v. 21, n. 6, p. 369, doi. 10.1093/protein/gzn012

By:

Andrew M. Simms;
Rudesh D. Toofanny;
Catherine Kehl;
Noah C. Benson;
Valerie Daggett

Publication type:

Article

Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations.

Published in:

PEDS: Protein Engineering, Design & Selection, 2008, v. 21, n. 6, p. 353, doi. 10.1093/protein/gzn011

By:

David A.C. Beck;
Amanda L. Jonsson;
R. Dustin Schaeffer;
Kathryn A. Scott;
Ryan Day;
Rudesh D. Toofanny;
Darwin O.V. Alonso;
Valerie Daggett

Publication type:

Article

Message from the Editors.

Published in:

PEDS: Protein Engineering, Design & Selection, 2008, v. 21, n. 3, p. 129, doi. 10.1093/protein/gzn008

By:

Valerie Daggett;
Alan Fersht

Publication type:

Article

Different disease-causing mutations in transthyretin trigger the same conformational conversion.

Published in:

PEDS: Protein Engineering, Design & Selection, 2008, v. 21, n. 3, p. 187, doi. 10.1093/protein/gzm086

By:

Robert E. Steward;
Roger S. Armen;
Valerie Daggett

Publication type:

Article

Human islet amyloid polypeptide‐induced β‐cell cytotoxicity is linked to formation of α‐sheet structure.

Published in:

Protein Science: A Publication of the Protein Society, 2024, v. 33, n. 2, p. 1, doi. 10.1002/pro.4854

By:

Hsu, Cheng‐Chieh;
Templin, Andrew T.;
Prosswimmer, Tatum;
Shea, Dylan;
Li, Jinzheng;
Brooks‐Worrell, Barbara;
Kahn, Steven E.;
Daggett, Valerie

Publication type:

Article

Conserved patterns and interactions in the unfolding transition state across SH3 domain structural homologues.

Published in:

Protein Science: A Publication of the Protein Society, 2021, v. 30, n. 2, p. 391, doi. 10.1002/pro.3998

By:

Demakis, Cullen;
Childers, Matthew C.;
Daggett, Valerie

Publication type:

Article

Tumorigenic p53 mutants undergo common structural disruptions including conversion to α‐sheet structure.

Published in:

Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 9, p. 1983, doi. 10.1002/pro.3921

By:

Bromley, Dennis;
Daggett, Valerie

Publication type:

Article

Molecular mechanisms underlying deoxy-ADP.Pi activation of pre-powerstroke myosin.

Published in:

Protein Science: A Publication of the Protein Society, 2017, v. 26, n. 4, p. 749, doi. 10.1002/pro.3121

By:

Nowakowski, Sarah G.;
Regnier, Michael;
Daggett, Valerie

Publication type:

Article

Opinion: The present view of the mechanism of protein folding.

Published in:

Nature Reviews Molecular Cell Biology, 2003, v. 4, n. 6, p. 497, doi. 10.1038/nrm1126

By:

Daggett, Valerie;
Fersht, Alan

Publication type:

Article

A Carboxylate to Amide Substitution That Switches Protein Folds.

Published in:

Angewandte Chemie International Edition, 2018, v. 57, n. 39, p. 12795, doi. 10.1002/anie.201807723

By:

Gianni, Stefano;
McCully, Michelle E.;
Malagrinò, Francesca;
Bonetti, Daniela;
De Simone, Alfonso;
Brunori, Maurizio;
Daggett, Valerie

Publication type:

Article

BioEssays 12/2012.

Published in:

BioEssays, 2012, v. 34, n. 12, p. n/a, doi. 10.1002/bies.201290059

By:

Towse, Clare-Louise;
Daggett, Valerie

Publication type:

Article

When a domain is not a domain, and why it is important to properly filter proteins in databases.

Published in:

BioEssays, 2012, v. 34, n. 12, p. 1060, doi. 10.1002/bies.201200116

By:

Towse, Clare-Louise;
Daggett, Valerie

Publication type:

Article

Understanding protein unfolding from molecular simulations.

Published in:

WIREs: Computational Molecular Science, 2012, v. 2, n. 3, p. 405, doi. 10.1002/wcms.1088

By:

Toofanny, Rudesh D.;
Daggett, Valerie

Publication type:

Article

A Carboxylate to Amide Substitution That Switches Protein Folds.

Published in:

Angewandte Chemie, 2018, v. 130, n. 39, p. 12977, doi. 10.1002/ange.201807723

By:

Gianni, Stefano;
McCully, Michelle E.;
Malagrinò, Francesca;
Bonetti, Daniela;
De Simone, Alfonso;
Brunori, Maurizio;
Daggett, Valerie

Publication type:

Article

Species variation in PrP<sup>Sc</sup> protofibril models.

Published in:

Journal of Materials Science, 2008, v. 43, n. 10, p. 3625, doi. 10.1007/s10853-008-2578-1

By:

Scouras, Alexander D.;
Daggett, Valerie

Publication type:

Article

Layer‐By‐Layer Functionalized Gauze With Designed α‐Sheet Peptides Inhibits E. coli and S. aureus Biofilm Formation.

Published in:

Journal of Biomedical Materials Research, Part A, 2025, v. 113, n. 3, p. 1, doi. 10.1002/jbm.a.37879

By:

Nick, Sarah E.;
Bryers, James D.;
Daggett, Valerie

Publication type:

Article

DIVE: a data intensive visualization engine.

Published in:

Bioinformatics, 2014, v. 30, n. 4, p. 593, doi. 10.1093/bioinformatics/btt721

By:

Bromley, Dennis;
Rysavy, Steven J.;
Su, Robert;
Toofanny, Rudesh D.;
Schmidlin, Tom;
Daggett, Valerie

Publication type:

Article

Generation of a consensus protein domain dictionary.

Published in:

Bioinformatics, 2011, v. 27, n. 1, p. 46, doi. 10.1093/bioinformatics/btq625

By:

Schaeffer, R. Dustin;
Jonsson, Amanda L.;
Simms, Andrew M.;
Daggett, Valerie

Publication type:

Article

Molecular Dynamics Simulations Capture the Misfolding of the Bovine Prion Protein at Acidic pH.

Published in:

Biomolecules (2218-273X), 2014, v. 4, n. 1, p. 181, doi. 10.3390/biom4010181

By:

Chin Jung Cheng;
Daggett, Valerie

Publication type:

Article

Different misfolding mechanisms converge on common conformational changes.

Published in:

Prion, 2014, v. 8, n. 1, p. 1, doi. 10.4161/pri.27807

By:

Jung Cheng, Chin;
Daggett, Valerie

Publication type:

Article

A molecular dynamics simulation of polyalanine: An analysis of equilibrium motions and helix-coil transitions.

Published in:

Biopolymers, 1991, v. 31, n. 9, p. 1115, doi. 10.1002/bip.360310911

By:

Daggett, Valerie;
Kollman, Peter A.;
Kuntz, Irwin D.

Publication type:

Article

Molecular dynamics simulations of small peptides: Dependence on dielectric model and pH.

Published in:

Biopolymers, 1991, v. 31, n. 3, p. 285, doi. 10.1002/bip.360310304

By:

Daggett, Valerie;
Kollman, Peter A.;
Kuntz, Irwin D.

Publication type:

Article

Loss of a metal-binding site in gelsolin leads to familial amyloidosis?Finnish type.

Published in:

Nature Structural Biology, 2002, v. 9, n. 2, p. 112, doi. 10.1038/nsb745

By:

Kazmirski, Steven L.;
Isaacson, Rivka L.;
An, Chahm;
Buckle, Ashley;
Johnson, Christopher M.;
Daggett, Valerie;
Fersht, Alan R.

Publication type:

Article

Peter Kollman.

Published in:

Nature Structural Biology, 2001, v. 8, n. 8, p. 662, doi. 10.1038/90356

By:

Levitt, Michael;
Daggett, Valerie

Publication type:

Article

Simulations of membrane-bound diglycosylated human prion protein reveal potential protective mechanisms against misfolding.

Published in:

Journal of Neurochemistry, 2017, v. 142, n. 1, p. 171, doi. 10.1111/jnc.14044

By:

Cheng, Chin Jung;
Koldsø, Heidi;
Van der Kamp, Marc W.;
Schiøtt, Birgit;
Daggett, Valerie

Publication type:

Article

Protein simulation data in the relational model.

Published in:

Journal of Supercomputing, 2012, v. 62, n. 1, p. 150, doi. 10.1007/s11227-011-0692-3

By:

Simms, Andrew;
Daggett, Valerie

Publication type:

Article

The complete folding pathway of a protein from nanoseconds to microseconds.

Published in:

Nature, 2003, v. 421, n. 6925, p. 863, doi. 10.1038/nature01428

By:

Mayor, Ugo;
Guydosh, Nicholas R.;
Johnson, Christopher M.;
Grossmann, J. Günter;
Sato, Satoshi;
Jas, Gouri S.;
Freund, Stefan M. V.;
Alonso, Darwin O. V.;
Daggett, Valerie;
Fersht, Alan R.

Publication type:

Article

Designed α-sheet peptides suppress amyloid formation in Staphylococcus aureus biofilms.

Published in:

NPJ Biofilms & Microbiomes, 2017, v. 3, n. 1, p. N.PAG, doi. 10.1038/s41522-017-0025-2

By:

Bleem, Alissa;
Francisco, Robyn;
Bryers, James D.;
Daggett, Valerie

Publication type:

Article

Conformational search using a molecular dynamics-minimization procedure: Applications to clusters of coulombic charges, Lennard-Jones particles, and waters.

Published in:

Journal of Computational Chemistry, 1998, v. 19, n. 1, p. 60, doi. 10.1002/(SICI)1096-987X(19980115)19:1<60::AID-JCC5>3.0.CO;2-X

By:

Li, Zhenqin;
Laidig, Keith E.;
Daggett, Valerie

Publication type:

Article