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List of works by Valerie Daggett

A Carboxylate to Amide Substitution That Switches Protein Folds

scientific article published on 28 August 2018

A Carboxylate to Amide Substitution That Switches Protein Folds

A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations ⬇️

scientific article published on April 24, 2012

A chemical group graph representation for efficient high-throughput analysis of atomistic protein simulations ⬇️

scientific article published on June 22, 2012

A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding

scientific article

A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary ⬇️

scientific article published on October 1, 2003

A hotspot of inactivation: The A22S and V108M polymorphisms individually destabilize the active site structure of catechol O-methyltransferase

scientific article

A microscopic view of peptide and protein solvation

scientific article

A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations

scientific article

A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8.

scientific article published on 12 November 2011

All-atom simulations of protein folding and unfolding

scientific article published on January 2003

Alpha-sheet: The toxic conformer in amyloid diseases?

scientific article

Altering Diffusivity in Biological Solutions through Modification of Solution Structure and Dynamics

scientific article (publication date: September 1998)

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

scientific article published on 08 August 2016

Analyzing disease-associated protein structures with visual analytics

scientific article

Anatomy of an amyloidogenic intermediate: conversion of beta-sheet to alpha-sheet structure in transthyretin at acidic pH.

scientific article

Cardiac myosin activation with 2-deoxy-ATP via increased electrostatic interactions with actin

scientific article published on 20 May 2019

Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases

scientific article

Characterization of cell-surface prion protein relative to its recombinant analogue: insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein

scientific article published on 23 February 2009

Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology

scientific article

Chemical and Physical Variability in Structural Isomers of an l/d α-Sheet Peptide Designed To Inhibit Amyloidogenesis

scientific article published on 4 December 2017

Combining experiment and simulation in protein folding: closing the gap for small model systems

scientific article

Conformational changes below the Tm: molecular dynamics studies of the thermal pretransition of ribonuclease A

scientific article published on 28 December 2007

Conformational entropy of alanine versus glycine in protein denatured states

scholarly article

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

scientific article published on 14 November 2020

Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution

scientific article

Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides

scientific article published in January 2005

DIVE: a data intensive visualization engine

scientific article

DIVE: a graph-based visual-analytics framework for big data

scientific article

De Novo Designed α-Sheet Peptides Inhibit Functional Amyloid Formation of Streptococcus mutans Biofilms

scholarly article by Natasha Paranjapye published in October 2018

Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation

scientific article

Designed Trpzip-3 β-Hairpin Inhibits Amyloid Formation in Two Different Amyloid Systems

scientific article

Designed α-sheet peptides inhibit amyloid formation by targeting toxic oligomers

scientific article

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

scientific article published on 3 July 2017

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

scientific article

Different misfolding mechanisms converge on common conformational changes: human prion protein pathogenic mutants Y218N and E196K.

scientific article

Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein

scientific article

Direct observation of microscopic reversibility in single-molecule protein folding

scientific article published on 15 November 2006

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

scientific article published on March 23, 2012

Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances

scientific article

Diverse effects on the native β-sheet of the human prion protein due to disease-associated mutations

scientific article

Drivers of α-Sheet Formation in Transthyretin under Amyloidogenic Conditions

scientific article published on 25 October 2019

Dynameomics: a comprehensive database of protein dynamics

scientific article

Dynameomics: a consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds

scientific article published on December 2009

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

scientific article

Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.

scientific article

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

scientific article

Dynameomics: large-scale assessment of native protein flexibility

scientific article published on 16 September 2008

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

scientific article published on 14 April 2008

Dynameomics: protein dynamics and unfolding across fold space

scientific article published in December 2010

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

scientific article published on June 19, 2013

Ensemble versus single-molecule protein unfolding

scientific article

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations

scientific article published on 11 October 2006

Folding mechanisms of proteins with high sequence identity but different folds.

scientific article

Formation of ice-like water structure on the surface of an antifreeze protein

scientific article published on 13 March 2008

Four human thiopurine s-methyltransferase alleles severely affect protein structure and dynamics

scientific article

From conversion to aggregation: protofibril formation of the prion protein

scholarly article

GB1 is not a two-state folder: identification and characterization of an on-pathway intermediate

scientific article

Generation of a consensus protein domain dictionary

scientific article

Identification of Multiple Folding Pathways Shared by Three-Helix Bundle Proteins

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

scientific article

Importance of context in protein folding: secondary structural propensities versus tertiary contact-assisted secondary structure formation

scientific article

Increasing temperature accelerates protein unfolding without changing the pathway of unfolding

scientific article

Influence of pH on the human prion protein: insights into the early steps of misfolding

scientific article

Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations

scientific article

Insights from molecular dynamics simulations for computational protein design

scientific article

Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series

scientific article published in January 2016

Introduction to special issue 'Three Decades of Protein Engineering: Impact on Structural Biology and Therapy' ⬇️

scientific article published on January 1, 2011

Is there a unifying mechanism for protein folding?

scientific article

Local environmental effects on the structure of the prion protein

scientific article

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

scientific article

Malleability of folding intermediates in the homeodomain superfamily

scientific article

Manifestations of native topology in the denatured state ensemble of Rhodopseudomonas palustris cytochrome c'.

scientific article published on 20 January 2011

Methods for molecular dynamics simulations of protein folding/unfolding in solution

scientific article

Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain

scientific article

Modeling Protein Folding Pathways

Molecular basis for the extensibility of elastin

scientific article

Molecular basis for the structural instability of human DJ-1 induced by the L166P mutation associated with Parkinson's disease

scientific article published on 16 August 2008

Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations

scientific article published on January 2011

Molecular dynamics simulations capture the misfolding of the bovine prion protein at acidic pH

scientific article

Molecular dynamics simulations of the protein unfolding/folding reaction

scientific article

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

scientific article published on 01 June 2018

Molecular mechanism for low pH triggered misfolding of the human prion protein

scientific article

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

scientific article published on 18 January 2017

Multimolecule test-tube simulations of protein unfolding and aggregation ⬇️

scientific article published on October 22, 2012

Myosin dynamics during relaxation in mouse soleus muscle and modulation by 2'-deoxy-ATP

scientific article published on 20 August 2020

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

scientific article

New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities

scientific article

Pathogenic mutations in the hydrophobic core of the human prion protein can promote structural instability and misfolding

scientific article

Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease

scientific article

Peptides Composed of Alternating L- and D-Amino Acids Inhibit Amyloidogenesis in Three Distinct Amyloid Systems Independent of Sequence

scientific article published on 21 March 2016

Phi-analysis at the experimental limits: mechanism of beta-hairpin formation

scientific article

Polymorphisms and disease: hotspots of inactivation in methyltransferases

scientific article

Preventing misfolding of the prion protein by trimethylamine N-oxide

scientific article

Principles of Ligand Binding within a Completely Buried Cavity in HIF2α PAS-B

scientific article

Probing the energy landscape of protein folding/unfolding transition states

scientific article published in May 2002

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

scientific article

Protein Engineering Reveals Mechanisms of Functional Amyloid Formation in Pseudomonas aeruginosa Biofilms

scholarly article by Alissa Bleem published in October 2018

Protein Folding: Molecular Dynamics Simulations

article

Protein Simulation Data in the Relational Model

scientific article

Protein Unfolding Pathways Explored Through Molecular Dynamics Simulations ⬇️

scientific article published on July 20, 1993

Protein conformation and diagnostic tests: the prion protein.

scientific article

Protein folding and binding: moving into unchartered territory

scientific article published on 13 February 2009

Protein folding and unfolding at atomic resolution

scientific article

Protein folding-simulation

scientific article

Protein folds and protein folding

scientific article

Refolding the Engrailed Homeodomain: Structural Basis for the Accumulation of a Folding Intermediate ⬇️

scientific article published on September 8, 2010

Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent

scientific article published in May 2005

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

scientific article published on 01 December 2019

Shedding light on amyloidosis with protein engineering

scientific article published in August 2009

Side-chain dynamics are critical for water permeation through aquaporin-1.

scientific article

Simulation and experiment at high temperatures: ultrafast folding of a thermophilic protein by nucleation-condensation

scientific article published in April 2005

Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding

scientific article published in July 2005

Simulations of biomolecules: Characterization of the early steps in the pH-induced conformational conversion of the hamster, bovine and human forms of the prion protein

scientific article

Simulations of macromolecules in protective and denaturing osmolytes: properties of mixed solvent systems and their effects on water and protein structure and dynamics.

scientific article

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

scientific article published on 13 April 2017

Stabilization of globular proteins via introduction of temperature-activated elastin-based switches

scientific article

Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains

scientific article

Structural Consequences of Mutations to the α-Tocopherol Transfer Protein Associated with the Neurodegenerative Disease Ataxia with Vitamin E Deficiency ⬇️

scientific article published on June 10, 2013

Structural Effects of the L145Q, V157F, and R282W Cancer-Associated Mutations in the p53 DNA-Binding Core Domain ⬇️

scientific article published on May 17, 2011

Structural and Functional Consequences of the Cardiac Troponin C L48Q Ca2+-Sensitizing Mutation ⬇️

scientific article published on May 23, 2012

Structural and dynamic properties of the human prion protein

scientific article

Structural and functional consequences of cardiac troponin C L57Q and I61Q Ca2+-desensitizing variants ⬇️

scientific article published on February 28, 2013

Structural and functional diversity among amyloid proteins: Agents of disease, building blocks of biology, and implications for molecular engineering

scientific article

Structural changes to monomeric CuZn superoxide dismutase caused by the familial amyotrophic lateral sclerosis-associated mutation A4V.

scientific article published on September 2009

Structural properties of prion protein protofibrils and fibrils: an experimental assessment of atomic models

scientific article

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

scientific article

Testing protein-folding simulations by experiment: B domain of protein A.

scientific article

The 108M polymorph of human catechol O-methyltransferase is prone to deformation at physiological temperatures

scientific article published in February 2006

The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space

scientific article

The R46Q, R131Q and R154H polymorphs of human DNA glycosylase/beta-lyase hOgg1 severely distort the active site and DNA recognition site but do not cause unfolding

scientific article published on July 2009

The Role of α-sheet in Amyloid Oligomer Aggregation and Toxicity

article

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

scientific article published on 03 October 2009

The complete folding pathway of a protein from nanoseconds to microseconds

scientific article published in February 2003

The consequences of pathogenic mutations to the human prion protein

scientific article published on 14 July 2009

The denatured state dictates the topology of two proteins with almost identical sequence but different native structure and function

scientific article

The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water ⬇️

scientific article published on February 1, 2011

The early steps in the unfolding of azurin

scientific article

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

scientific article

The effect of context on the folding of β-hairpins ⬇️

scientific article published on August 6, 2011

The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment

scientific article

The histamine N-methyltransferase T105I polymorphism affects active site structure and dynamics

scientific article

The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR.

scientific article

The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins

scientific article

The molecular basis for the chemical denaturation of proteins by urea ⬇️

scientific article published on April 17, 2003

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

scientific article

The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea

scientific article (publication date: 20 February 2002)

The present view of the mechanism of protein folding

scientific article

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

scientific article published on January 2010

The role of alpha-, 3(10)-, and pi-helix in helix-->coil transitions

scientific article

The role of the turn in beta-hairpin formation during WW domain folding

scientific article published on 31 August 2007

The structure of the major transition state for folding of an FF domain from experiment and simulation

scientific article published in July 2005

Tumorigenic p53 Mutants Undergo Common Structural Disruptions Including Conversion to α-Sheet Structure

scientific article published on 26 July 2020

Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein

scientific article

Unifying features in protein-folding mechanisms

scientific article published on 31 October 2003

Using flexible loop mimetics to extend  -value analysis to secondary structure interactions

scientific article

Using simulations to provide the framework for experimental protein folding studies

scientific article

Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles

article

Visualizing Protein Folding and Unfolding

scientific article published on 03 March 2019

Wavelet Analysis of Protein Motion

scientific article

When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative

scientific article published on 26 October 2012

α-Sheet secondary structure in amyloid β-peptide drives aggregation and toxicity in Alzheimer's disease

scientific article published on 19 April 2019

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