January 2, 2025, Filed Under: 2003, PublicationsThe dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study. Citation: Tobi, D. ; Elber, R. ; Thirumalai, D. The dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study. Biopolymers 68, 359-69. Download the-dominant-interaction-between-peptide-and-urea-is-electrostatic-in-nature-a-molecular-dynamics-simulation-study.pdf5.39 MB Last updated on 01/03/2018 PubMed DOI
January 2, 2025, Filed Under: 2003, PublicationsEmerging ideas on the molecular basis of protein and peptide aggregation. Citation: Thirumalai, D. ; Klimov, D. K. ; Dima, R. I. Emerging ideas on the molecular basis of protein and peptide aggregation. Curr Opin Struct Biol 13, 146-59. Download emerging-ideas-on-the-molecular-basis-of-protein-and-peptide-aggregation.pdf686 KB Last updated on 01/03/2018 PubMed
January 2, 2025, Filed Under: 2003, PublicationsMolecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. Citation: Mountain, R. D. ; Thirumalai, D. Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. J Am Chem Soc 125, 1950-7. Download Citation molecular-dynamics-simulations-of-end-to-end-contact-formation-in-hydrocarbon-chains-in-water-and-aqueous-urea-solution.pdf201 KB Last updated on 08/18/2017 PubMed DOI
January 2, 2025, Filed Under: 2002, PublicationsCharge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer’s beta-amyloid peptide compared to E22Q Dutch mutant. Citation: Massi, F. ; Klimov, D. ; Thirumalai, D. ; Straub, J. E. Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer’s beta-amyloid peptide compared to E22Q Dutch mutant. Protein Sci 11, 1639-47. Download charge-states-rather-than-propensity-for-beta-structure-determine-enhanced-fibrillogenesis-in-wild-type-alzheimers-beta-amyloid-peptide-compared-to-e22q-dutch-mutant.pdf541 KB Last updated on 01/03/2018 PubMed DOI
January 2, 2025, Filed Under: 2002, PublicationsExploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Citation: Dima, R. I. ; Thirumalai, D. Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics. Protein Sci 11, 1036-49. Download exploring-protein-aggregation-and-self-propagation-using-lattice-models-phase-diagram-and-kinetics.pdf273 KB Last updated on 01/03/2018 PubMed DOI
January 2, 2025, Filed Under: 2002, PublicationsSimulations of beta-hairpin folding confined to spherical pores using distributed computing. Citation: Klimov, D. K. ; Newfield, D. ; Thirumalai, D. Simulations of beta-hairpin folding confined to spherical pores using distributed computing. Proc Natl Acad Sci U S A 99, 8019-24. Download simulations-of-beta-hairpin-folding-confined-to-spherical-pores-using-distributed-computing.pdf318 KB Last updated on 01/03/2018 PubMed DOI
January 2, 2025, Filed Under: 2002, PublicationsStiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. Citation: Klimov, D. K. ; Thirumalai, D. Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J Mol Biol 317, 721-37. Download Citation PubMed DOI
January 2, 2025, Filed Under: 2002, PublicationsIs there a unique melting temperature for two-state proteins? Citation: Klimov, D. K. ; Thirumalai, D. Is there a unique melting temperature for two-state proteins?. J Comput Chem 23, 161-5. Download Citation PubMed DOI
January 2, 2025, Filed Under: 2002, PublicationsExploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. Citation: Dima, R. I. ; Thirumalai, D. Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. Biophys J 83, 1268-80. Download exploring-the-propensities-of-helices-in-prpc-to-form-beta-sheet-using-nmr-structures-and-sequence-alignments.pdf541 KB Last updated on 01/03/2018 PubMed DOI
January 2, 2025, Filed Under: 2001, PublicationsRole of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. Citation: Heilman-Miller, S. L. ; Thirumalai, D. ; Woodson, S. A. Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. J Mol Biol 306, 1157-66. Download role-of-counterion-condensation-in-folding-of-the-tetrahymena-ribozyme-ii-counterion-dependence-of-folding-kinetics.pdf305 KB Last updated on 01/03/2018 PubMed DOI
