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Valerie Daggett

Research Profile

Concepts & Ideas

Physiology

Protein Folding

Activities & Behaviors

Disorders

Protein Denaturation

Chemicals & Drugs

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Thermodynamics

Genes & Molecular Sequences

Amino Acid Sequences

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Publications

TOP 3
Dan Wang; An-Yue Tu; Valerie Daggett; Zhaoxiong Luo; Michelle E McCully; Jonathan McMichael; Michael Regnier
Structural and functional consequences of cardiac troponin C L57Q and I61Q Ca(2+)-desensitizing variants.
Michelle E McCully; David A C Beck; Valerie Daggett
Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain.
Clare-Louise Towse; Valerie Daggett
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.

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All Publications

2013: Dan Wang; An-Yue Tu; Valerie Daggett; Zhaoxiong Luo; Michelle E McCully; Jonathan McMichael; Michael Regnier
Structural and functional consequences of cardiac troponin C L57Q and I61Q Ca(2+)-desensitizing variants.
Archives of biochemistry and biophysics 2013;535(1):68-75.
2013: Michelle E McCully; David A C Beck; Valerie Daggett
Promiscuous contacts and heightened dynamics increase thermostability in an engineered variant of the engrailed homeodomain.
Protein engineering, design & selection : PEDS 2013;26(1):35-45.
2012: Clare-Louise Towse; Valerie Daggett
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.
BioEssays : news and reviews in molecular, cellular and developmental biology 2012;34(12):1060-9.
2012: Michelle E McCully; David A C Beck; Valerie Daggett
Multimolecule test-tube simulations of protein unfolding and aggregation.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(44):17851-6.
2012: Noah C Benson; Valerie Daggett
A chemical group graph representation for efficient high-throughput analysis of atomistic protein simulations.
Journal of bioinformatics and computational biology 2012;10(4):1250008.
2012: Noah C Benson; Valerie Daggett
A comparison of multiscale methods for the analysis of molecular dynamics simulations.
The journal of physical chemistry. B 2012;116(29):8722-31.
2012: Alexander D Scouras; Valerie Daggett
Disruption of the X-loop turn of the prion protein linked to scrapie resistance.
Protein engineering, design & selection : PEDS 2012;25(5):243-9.
2011: Amanda L Jonsson; Valerie Daggett
The effect of context on the folding of β-hairpins.
Journal of structural biology 2011;176(2):143-50.
2011: Sara Calhoun; Valerie Daggett
Structural effects of the L145Q, V157F, and R282W cancer-associated mutations in the p53 DNA-binding core domain.
Biochemistry 2011;50(23):5345-53.
2011: Wiktor Banachewicz; Tomasz L Religa; R D Schaeffer; Valerie Daggett; Alan R Fersht
Malleability of folding intermediates in the homeodomain superfamily.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(14):5596-601.
2011: Alexander D Scouras; Valerie Daggett
The Dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water.
Protein science : a publication of the Protein Society 2011;20(2):341-52.
2011: Rudesh D Toofanny; Andrew Simms; David A C Beck; Valerie Daggett
Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.
BMC bioinformatics 2011;12():334.
2011: Marc W van der Kamp; Valerie Daggett
Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations.
Topics in current chemistry 2011;305():169-97.
2011: R Dustin Schaeffer; Amanda L Jonsson; Andrew Simms; Valerie Daggett
Generation of a consensus protein domain dictionary.
Bioinformatics (Oxford, England) 2011;27(1):46-54.
2011: R Dustin Schaeffer; Valerie Daggett
Protein folds and protein folding.
Protein engineering, design & selection : PEDS 2011;24(1-2):11-9.
2010: Wei Chen; Marc Van der Kamp; Valerie Daggett
Diverse effects on the native β-sheet of the human prion protein due to disease-associated mutations.
Biochemistry 2010;49(45):9874-81.
2010: Marc Van der Kamp; Valerie Daggett
Influence of pH on the human prion protein: insights into the early steps of misfolding.
Biophysical journal 2010;99(7):2289-98.
2010: Karen Rutherford; Valerie Daggett
Polymorphisms and disease: hotspots of inactivation in methyltransferases.
Trends in biochemical sciences 2010;35(10):531-8.
2010: Rudesh D Toofanny; Amanda L Jonsson; Valerie Daggett
A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding.
Biophysical journal 2010;98(11):2671-81.
2010: Eric D Merkley; William W Parson; Valerie Daggett
Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold.
Protein engineering, design & selection : PEDS 2010;23(5):327-36.
2010: Marc Van der Kamp; R Dustin Schaeffer; Amanda L Jonsson; Alexander D Scouras; Andrew Simms; Rudesh D Toofanny; Noah C Benson; Peter C Anderson; Eric D Merkley; Steven Rysavy; Dennis Bromley; David A C Beck; Valerie Daggett
Dynameomics: a comprehensive database of protein dynamics.
Structure (London, England : 1993) 2010;18(4):423-35.
2010: Peter B Law; Valerie Daggett
The relationship between water bridges and the polyproline II conformation: a large-scale analysis of molecular dynamics simulations and crystal structures.
Protein engineering, design & selection : PEDS 2010;23(1):27-33.
2009: Jason Key; Thomas H Scheuermann; Peter C Anderson; Valerie Daggett; Kevin H Gardner
Principles of ligand binding within a completely buried cavity in HIF2alpha PAS-B.
Journal of the American Chemical Society 2009;131(48):17647-54.
2009: Amanda L Jonsson; Kathryn A Scott; Valerie Daggett
Dynameomics: a consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds.
Biophysical journal 2009;97(11):2958-66.
2009: Karen Rutherford; Valerie Daggett
The V119I polymorphism in protein L-isoaspartate O-methyltransferase alters the substrate-binding interface.
Protein engineering, design & selection : PEDS 2009;22(12):713-21.
2009: Tom Schmidlin; Brian Kennedy; Valerie Daggett
Structural changes to monomeric CuZn superoxide dismutase caused by the familial amyotrophic lateral sclerosis-associated mutation A4V.
Biophysical journal 2009;97(6):1709-18.
2009: Marc Van der Kamp; Valerie Daggett
The consequences of pathogenic mutations to the human prion protein.
Protein engineering, design & selection : PEDS 2009;22(8):461-8.
2009: Mari L DeMarco; Valerie Daggett
Characterization of cell-surface prion protein relative to its recombinant analogue: insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein.
Journal of neurochemistry 2009;109(1):60-73.
2009: Valerie Daggett; Alan Fersht
Protein folding and binding: moving into unchartered territory.
Current opinion in structural biology 2009;19(1):1-2.
2008: David A C Beck; Darwin O V Alonso; Daigo Inoyama; Valerie Daggett
The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(34):12259-64.
2008: Nikolai Smolin; Bin Li; David A C Beck; Valerie Daggett
Side-chain dynamics are critical for water permeation through aquaporin-1.
Biophysical journal 2008;95(3):1089-98.
2008: Michelle E McCully; David A C Beck; Valerie Daggett
Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain.
Biochemistry 2008;47(27):7079-89.
2008: K Rutherford; E Alphandéry; A McMillan; Valerie Daggett; William W Parson
The V108M mutation decreases the structural stability of catechol O-methyltransferase.
Biochimica et biophysica acta 2008;1784(7-8):1098-105.
2008: Karen Rutherford; Valerie Daggett
Four human thiopurine s-methyltransferase alleles severely affect protein structure and dynamics.
Journal of molecular biology 2008;379(4):803-14.
2008: David A C Beck; Amanda L Jonsson; R Dustin Schaeffer; Kathryn A Scott; Ryan Day; Rudesh D Toofanny; Darwin O V Alonso; Valerie Daggett
Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations.
Protein engineering, design & selection : PEDS 2008;21(6):353-68.
2008: Andrew Simms; Rudesh D Toofanny; Catherine Kehl; Noah C Benson; Valerie Daggett
Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations.
Protein engineering, design & selection : PEDS 2008;21(6):369-77.
2008: Nikolai Smolin; Valerie Daggett
Formation of ice-like water structure on the surface of an antifreeze protein.
The journal of physical chemistry. B 2008;112(19):6193-202.
2008: Robert E Steward; Roger S Armen; Valerie Daggett
Different disease-causing mutations in transthyretin trigger the same conformational conversion.
Protein engineering, design & selection : PEDS 2008;21(3):187-95.
2008: R Dustin Schaeffer; Alan Fersht; Valerie Daggett
Combining experiment and simulation in protein folding: closing the gap for small model systems.
Current opinion in structural biology 2008;18(1):4-9.
2008: Eric D Merkley; Brady Bernard; Valerie Daggett
Conformational changes below the Tm: molecular dynamics studies of the thermal pretransition of ribonuclease A.
Biochemistry 2008;47(3):880-92.
2008: Karen Rutherford; William W Parson; Valerie Daggett
The histamine N-methyltransferase T105I polymorphism affects active site structure and dynamics.
Biochemistry 2008;47(3):893-901.
2007: David A C Beck; Valerie Daggett
A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations.
Biophysical journal 2007;93(10):3382-91.
2007: Mari L DeMarco; Valerie Daggett
Molecular mechanism for low pH triggered misfolding of the human prion protein.
Biochemistry 2007;46(11):3045-54.
2007: David A C Beck; George W N White; Valerie Daggett
Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.
Journal of structural biology 2007;157(3):514-23.
2007: Kathryn A Scott; Darwin O V Alonso; Satoshi Sato; Alan Fersht; Valerie Daggett
Conformational entropy of alanine versus glycine in protein denatured states.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(8):2661-6.
2007: Ryan Day; Valerie Daggett
Direct observation of microscopic reversibility in single-molecule protein folding.
Journal of molecular biology 2007;366(2):677-86.
2007: Kathryn A Scott; Valerie Daggett
Folding mechanisms of proteins with high sequence identity but different folds.
Biochemistry 2007;46(6):1545-56.
2007: David A C Beck; Brian J Bennion; Darwin O V Alonso; Valerie Daggett
Simulations of macromolecules in protective and denaturing osmolytes: properties of mixed solvent systems and their effects on water and protein structure and dynamics.
Methods in enzymology 2007;428():373-96.
2006: Mari L DeMarco; Jay Silveira; Byron Caughey; Valerie Daggett
Structural properties of prion protein protofibrils and fibrils: an experimental assessment of atomic models.
Biochemistry 2006;45(51):15573-82.
2006: Valerie Daggett
Alpha-sheet: The toxic conformer in amyloid diseases?
Accounts of chemical research 2006;39(9):594-602.
2006: Valerie Daggett
Protein folding-simulation.
Chemical reviews 2006;106(5):1898-916.
2006: Kathryn A Scott; Darwin O V Alonso; Yongping Pan; Valerie Daggett
Importance of context in protein folding: secondary structural propensities versus tertiary contact-assisted secondary structure formation.
Biochemistry 2006;45(13):4153-63.
2006: Karen Rutherford; Brian J Bennion; William W Parson; Valerie Daggett
The 108M polymorph of human catechol O-methyltransferase is prone to deformation at physiological temperatures.
Biochemistry 2006;45(7):2178-88.
2005: Roger S Armen; Valerie Daggett
Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology.
Biochemistry 2005;44(49):16098-107.
2005: Mari L DeMarco; Valerie Daggett
Local environmental effects on the structure of the prion protein.
Comptes rendus biologies 2005;328(10-11):847-62.
2005: Roger S Armen; Brady M Bernard; Ryan Day; Darwin O V Alonso; Valerie Daggett
Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(38):13433-8.
2005: Ryan Day; Valerie Daggett
Ensemble versus single-molecule protein unfolding.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(38):13445-50.
2005: George W N White; Stefano Gianni; J Günter Grossmann; Per Jemth; Alan Fersht; Valerie Daggett
Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding.
Journal of molecular biology 2005;350(4):757-75.
2005: Per Jemth; Ryan Day; Stefano Gianni; Faaizah Khan; Mark Allen; Valerie Daggett; Alan Fersht
The structure of the major transition state for folding of an FF domain from experiment and simulation.
Journal of molecular biology 2005;350(2):363-78.
2005: Ryan Day; Valerie Daggett
Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent.
Protein science : a publication of the Protein Society 2005;14(5):1242-52.
2005: David A C Beck; Roger S Armen; Valerie Daggett
Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides.
Biochemistry 2005;44(2):609-16.
2004: Brian J Bennion; Mari L DeMarco; Valerie Daggett
Preventing misfolding of the prion protein by trimethylamine N-oxide.
Biochemistry 2004;43(41):12955-63.
2004: Roger S Armen; Darwin O V Alonso; Valerie Daggett
Anatomy of an amyloidogenic intermediate: conversion of beta-sheet to alpha-sheet structure in transthyretin at acidic pH.
Structure (London, England : 1993) 2004;12(10):1847-63.
2004: David A C Beck; Valerie Daggett
Methods for molecular dynamics simulations of protein folding/unfolding in solution.
Methods (San Diego, Calif.) 2004;34(1):112-20.
2004: Mari L DeMarco; Darwin O V Alonso; Valerie Daggett
Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein.
Journal of molecular biology 2004;341(4):1109-24.
2004: Roger S Armen; Mari L DeMarco; Darwin O V Alonso; Valerie Daggett
Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(32):11622-7.
2004: Satoshi Sato; Tomasz L Religa; Valerie Daggett; Alan Fersht
Testing protein-folding simulations by experiment: B domain of protein A.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(18):6952-6.
2004: Per Jemth; Stefano Gianni; Ryan Day; Bin Li; Christopher M Johnson; Valerie Daggett; Alan Fersht
Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(17):6450-5.
2004: Brian J Bennion; Valerie Daggett
Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(17):6433-8.
2004: Mari L DeMarco; Valerie Daggett
From conversion to aggregation: protofibril formation of the prion protein.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(8):2293-8.
2003: Yongjin Zhu; Darwin O V Alonso; Kosuke Maki; Cheng-Yen Huang; Steven J Lahr; Valerie Daggett; Heinrich Roder; William F DeGrado; Feng Gai
Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(26):15486-91.
2003: Stefano Gianni; Nicholas R Guydosh; Faaizah Khan; Teresa D Caldas; Ugo Mayor; George W N White; Mari L DeMarco; Valerie Daggett; Alan Fersht
Unifying features in protein-folding mechanisms.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(23):13286-91.
2003: Ryan Day; David A C Beck; Roger S Armen; Valerie Daggett
A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.
Protein science : a publication of the Protein Society 2003;12(10):2150-60.
2003: Valerie Daggett; Alan Fersht
The present view of the mechanism of protein folding.
Nature reviews. Molecular cell biology 2003;4(6):497-502.
2003: Roger S Armen; Darwin O V Alonso; Valerie Daggett
The role of alpha-, 3(10)-, and pi-helix in helix-->coil transitions.
Protein science : a publication of the Protein Society 2003;12(6):1145-57.
2003: Brian J Bennion; Valerie Daggett
The molecular basis for the chemical denaturation of proteins by urea.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(9):5142-7.
2003: Scott T R Walsh; Richard P Cheng; Wayne W Wright; Darwin O V Alonso; Valerie Daggett; Jane M Vanderkooi; William F DeGrado
The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR.
Protein science : a publication of the Protein Society 2003;12(3):520-31.
2003: Ugo Mayor; Nicholas R Guydosh; Christopher M Johnson; J Günter Grossmann; Satoshi Sato; Gouri S Jas; Stefan M V Freund; Darwin O V Alonso; Valerie Daggett; Alan Fersht
The complete folding pathway of a protein from nanoseconds to microseconds.
Nature 2003;421(6925):863-7.
2003: Ryan Day; Valerie Daggett
All-atom simulations of protein folding and unfolding.
Advances in protein chemistry 2003;66():373-403.
2003: David A C Beck; Darwin O V Alonso; Valerie Daggett
A microscopic view of peptide and protein solvation.
Biophysical chemistry 2003;100(1-3):221-37.
2003: Bin Li; Valerie Daggett
The molecular basis of the temperature- and pH-induced conformational transitions in elastin-based peptides.
Biopolymers 2003;68(1):121-9.
2003: Valerie Daggett; Alan Fersht
Is there a unifying mechanism for protein folding?
Trends in biochemical sciences 2003;28(1):18-25.
2002: Brian J Bennion; Valerie Daggett
Protein conformation and diagnostic tests: the prion protein.
Clinical chemistry 2002;48(12):2105-14.
2002: Ryan Day; Brian J Bennion; Sihyun Ham; Valerie Daggett
Increasing temperature accelerates protein unfolding without changing the pathway of unfolding.
Journal of molecular biology 2002;322(1):189-203.
2002: Bin Li; Darwin O V Alonso; Valerie Daggett
Stabilization of globular proteins via introduction of temperature-activated elastin-based switches.
Structure (London, England : 1993) 2002;10(7):989-98.
2002: Darwin O V Alonso; Chahm An; Valerie Daggett
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.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 2002;360(1795):1165-78.
2002: Valerie Daggett
Molecular dynamics simulations of the protein unfolding/folding reaction.
Accounts of chemical research 2002;35(6):422-9.
2002: Deborah De Jong; Robert Riley; Darwin O V Alonso; Valerie Daggett
Probing the energy landscape of protein folding/unfolding transition states.
Journal of molecular biology 2002;319(1):229-42.
2002: Qin Zou; Brian J Bennion; Valerie Daggett; Kenneth P Murphy
The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea.
Journal of the American Chemical Society 2002;124(7):1192-202.
2002: Steven L Kazmirski; Rivka L Isaacson; Chahm An; Ashley M Buckle; Christopher M Johnson; Valerie Daggett; Alan Fersht
Loss of a metal-binding site in gelsolin leads to familial amyloidosis-Finnish type.
Nature structural biology 2002;9(2):112-6.
2002: Bin Li; Valerie Daggett
Molecular basis for the extensibility of elastin.
Journal of muscle research and cell motility 2002;23(5-6):561-73.
2001: Bin Li; Darwin O V Alonso; Brian J Bennion; Valerie Daggett
Hydrophobic hydration is an important source of elasticity in elastin-based biopolymers.
Journal of the American Chemical Society 2001;123(48):11991-8.
2001: Steven L Kazmirski; Kam-Bo Wong; Stefan M V Freund; Y J Tan; Alan Fersht; Valerie Daggett
Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(8):4349-54.
2001: Darwin O V Alonso; S J DeArmond; Fred Cohen; Valerie Daggett
Mapping the early steps in the pH-induced conformational conversion of the prion protein.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(6):2985-9.
2001: Y Pan; Valerie Daggett
Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding.
Biochemistry 2001;40(9):2723-31.
2001: Bin Li; Darwin O V Alonso; Valerie Daggett
The molecular basis for the inverse temperature transition of elastin.
Journal of molecular biology 2001;305(3):581-92.
2001: Darwin O V Alonso; Valerie Daggett
Simulations and computational analyses of prion protein conformations.
Advances in protein chemistry 2001;57():107-37.
2000: Ugo Mayor; Christopher M Johnson; Valerie Daggett; Alan Fersht
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(25):13518-22.
2000: J Clarke; A M Hounslow; CJ Bond; Alan Fersht; Valerie Daggett
The effects of disulfide bonds on the denatured state of barnase.
Protein science : a publication of the Protein Society 2000;9(12):2394-404.
2000: Valerie Daggett
Long timescale simulations.
Current opinion in structural biology 2000;10(2):160-4.
2000: Kam-Bo Wong; J Clarke; CJ Bond; J L Neira; Stefan M V Freund; Alan Fersht; Valerie Daggett
Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding.
Journal of molecular biology 2000;296(5):1257-82.
2000: Darwin O V Alonso; Eric J Alm; Valerie Daggett
Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: implications for domain swapping.
Structure (London, England : 1993) 2000;8(1):101-10.
2000: Darwin O V Alonso; Valerie Daggett
Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(1):133-8.
1999: Steven L Kazmirski; A Li; Valerie Daggett
Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles.
Journal of molecular biology 1999;290(1):283-304.
1999: E M Storch; Jeffrey S Grinstead; A Patricia Campbell; Valerie Daggett; William M Atkins
Engineering out motion: a surface disulfide bond alters the mobility of tryptophan 22 in cytochrome b5 as probed by time-resolved fluorescence and 1H NMR experiments.
Biochemistry 1999;38(16):5065-75.
1999: E M Storch; Valerie Daggett; William M Atkins
Engineering out motion: introduction of a de novo disulfide bond and a salt bridge designed to close a dynamic cleft on the surface of cytochrome b5.
Biochemistry 1999;38(16):5054-64.
1998: Steven L Kazmirski; Valerie Daggett
Non-native interactions in protein folding intermediates: molecular dynamics simulations of hen lysozyme.
Journal of molecular biology 1998;284(3):793-806.
1998: Kam-Bo Wong; Valerie Daggett
Barstar has a highly dynamic hydrophobic core: evidence from molecular dynamics simulations and nuclear magnetic resonance relaxation data.
Biochemistry 1998;37(32):11182-92.
1998: Valerie Daggett
Structure-function aspects of prion proteins.
Current opinion in biotechnology 1998;9(4):359-65.
1998: AG Ladurner; LS Itzhaki; Valerie Daggett; Alan Fersht
Synergy between simulation and experiment in describing the energy landscape of protein folding.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(15):8473-8.
1998: Darwin O V Alonso; Valerie Daggett
Molecular dynamics simulations of hydrophobic collapse of ubiquitin.
Protein science : a publication of the Protein Society 1998;7(4):860-74.
1998: Steven L Kazmirski; Valerie Daggett
Simulations of the structural and dynamical properties of denatured proteins: the "molten coil" state of bovine pancreatic trypsin inhibitor.
Journal of molecular biology 1998;277(2):487-506.
1998: A Li; Valerie Daggett
Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate.
Journal of molecular biology 1998;275(4):677-94.
1997: CJ Bond; Kam-Bo Wong; J Clarke; Alan Fersht; Valerie Daggett
Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(25):13409-13.
1996: E M Storch; Valerie Daggett
Structural consequences of heme removal: molecular dynamics simulations of rat and bovine apocytochrome b5.
Biochemistry 1996;35(36):11596-604.
1996: Valerie Daggett; A Li; LS Itzhaki; D E Otzen; Alan Fersht
Structure of the transition state for folding of a protein derived from experiment and simulation.
Journal of molecular biology 1996;257(2):430-40.
1996: A Li; Valerie Daggett
Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations.
Journal of molecular biology 1996;257(2):412-29.
1996: K E Laidig; Valerie Daggett
Molecular dynamics simulations of apocytochrome b562--the highly ordered limit of molten globules.
Folding & design 1996;1(5):335-46.
1995: A Li; Valerie Daggett
Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: comparison to x-ray crystallographic and NMR data.
Protein engineering 1995;8(11):1117-28.
1995: E M Storch; Valerie Daggett
Molecular dynamics simulation of cytochrome b5: implications for protein-protein recognition.
Biochemistry 1995;34(30):9682-93.
1995: Kent Kirshenbaum; Valerie Daggett
Sequence effects on the conformational properties of the amyloid beta (1-28) peptide: testing a proposed mechanism for the alpha-->beta transition.
Biochemistry 1995;34(23):7640-7.
1995: Kent Kirshenbaum; Valerie Daggett
pH-dependent conformations of the amyloid beta(1-28) peptide fragment explored using molecular dynamics.
Biochemistry 1995;34(23):7629-39.
1995: Steven L Kazmirski; D O Alonso; Fred Cohen; Stanley B Prusiner; Valerie Daggett
Theoretical studies of sequence effects on the conformational properties of a fragment of the prion protein: implications for scrapie formation.
Chemistry & biology 1995;2(5):305-15.
1995: D O Alonso; Valerie Daggett
Molecular dynamics simulations of protein unfolding and limited refolding: characterization of partially unfolded states of ubiquitin in 60% methanol and in water.
Journal of molecular biology 1995;247(3):501-20.
1994: A Li; Valerie Daggett
Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(22):10430-4.