Alonso DO - Search Results

1

Molecular dynamics simulations of hydrophobic collapse of ubiquitin.

Alonso DO, Daggett V. Alonso DO, et al. Protein Sci. 1998 Apr;7(4):860-74. doi: 10.1002/pro.5560070404. Protein Sci. 1998. PMID: 9568893 Free PMC article.

2

Probing the energy landscape of protein folding/unfolding transition states.

De Jong D, Riley R, Alonso DO, Daggett V. De Jong D, et al. Among authors: alonso do. J Mol Biol. 2002 May 24;319(1):229-42. doi: 10.1016/S0022-2836(02)00212-7. J Mol Biol. 2002. PMID: 12051948

3

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

Walsh ST, Cheng RP, Wright WW, Alonso DO, Daggett V, Vanderkooi JM, DeGrado WF. Walsh ST, et al. Among authors: alonso do. Protein Sci. 2003 Mar;12(3):520-31. doi: 10.1110/ps.0223003. Protein Sci. 2003. PMID: 12592022 Free PMC article.

4

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

Armen R, Alonso DO, Daggett V. Armen R, et al. Among authors: alonso do. Protein Sci. 2003 Jun;12(6):1145-57. doi: 10.1110/ps.0240103. Protein Sci. 2003. PMID: 12761385 Free PMC article.

5

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.

Alonso DO, An C, Daggett V. Alonso DO, et al. Philos Trans A Math Phys Eng Sci. 2002 Jun 15;360(1795):1165-78. doi: 10.1098/rsta.2002.0986. Philos Trans A Math Phys Eng Sci. 2002. PMID: 12804272

6

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

Scott KA, Alonso DO, Pan Y, Daggett V. Scott KA, et al. Among authors: alonso do. Biochemistry. 2006 Apr 4;45(13):4153-63. doi: 10.1021/bi0517281. Biochemistry. 2006. PMID: 16566589

7

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

Beck DA, Bennion BJ, Alonso DO, Daggett V. Beck DA, et al. Among authors: alonso do. Methods Enzymol. 2007;428:373-96. doi: 10.1016/S0076-6879(07)28022-X. Methods Enzymol. 2007. PMID: 17875430

8

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

Beck DA, Jonsson AL, Schaeffer RD, Scott KA, Day R, Toofanny RD, Alonso DO, Daggett V. Beck DA, et al. Among authors: alonso do. Protein Eng Des Sel. 2008 Jun;21(6):353-68. doi: 10.1093/protein/gzn011. Epub 2008 Apr 14. Protein Eng Des Sel. 2008. PMID: 18411224

9

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

Alonso DO, Daggett V. Alonso DO, et al. Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):133-8. doi: 10.1073/pnas.97.1.133. Proc Natl Acad Sci U S A. 2000. PMID: 10618383 Free PMC article.

10

Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: implications for domain swapping.

Alonso DO, Alm E, Daggett V. Alonso DO, et al. Structure. 2000 Jan 15;8(1):101-10. doi: 10.1016/s0969-2126(00)00083-6. Structure. 2000. PMID: 10673427 Free article.

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