Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK.
Bauer D., Merz D. R., Pelz B., Theisen K. E., Yacyshyn G., Mokranjac D., Dima R. I., Rief M., Žoldák G
Proc. Natl. Acad. Sci. USA 2015 Aug 18;112(33):10389-94. doi: 10.1073/pnas.1504625112
Pubmed
Molecular investigations into the mechanics of a muscle anchoring complex.
Bodmer N. K., Theisen K. E., Dima R. I.
Biophys J. 2015 May 5;108(9):2322-32. doi: 10.1016/j.bpj.2015.03.036
Pubmed
Stoichiometry and topology in protein folding.
Dima RI.
J Biomol Struct Dyn. 2011 Feb;28(4):617-8; discussion 669-674
Pubmed
Order statistics theory of unfolding of multimeric proteins.
Zhmurov A, Dima RI, Barsegov V.
Biophys J. 2010 Sep 22; 99(6):1959-68. doi: 10.1016/j.bpj.2010.07.012
Pubmed
Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors.
Zhmurov A, Dima RI, Kholodov Y, Barsegov V.
Proteins. 2010 Nov 1;78(14):2984-99. doi: 10.1002/prot.22824
Pubmed
Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations.
Mickler M, Dima RI, Dietz H, Hyeon C, Thirumalai D, Rief M.
Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20268-73
Pubmed
Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism.
O'Brien EP, Dima RI, Brooks B, Thirumalai D.
J Am Chem Soc. 2007 Jun 13;129(23):7346-53
Pubmed
Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back.
Chen J, Dima RI, Thirumalai D.
J Mol Biol. 2007 Nov 16;374(1):250-66
Pubmed
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins.
Hyeon C, Dima RI, Thirumalai D.
Structure. 2006 Nov;14(11):1633-45
Pubmed
Determination of network of residues that regulate allostery in protein families using sequence analysis.
Dima RI, Thirumalai D.
Protein Sci. 2006 Feb;15(2):258-68
Pubmed
Size, shape, and flexibility of RNA structures.
Hyeon C, Dima RI, Thirumalai D.
J Chem Phys. 2006 Nov 21;125(19):194905
Pubmed
Extracting stacking interaction parameters for RNA from the data set of native structures.
Dima RI, Hyeon C, Thirumalai D.
J Mol Biol. 2005 Mar 18;347(1):53-69
Pubmed
Proteins associated with diseases show enhanced sequence correlation between charged residues.
Dima RI, Thirumalai D.
Bioinformatics. 2004 Oct 12;20(15):2345-54
Pubmed
Probing the instabilities in the dynamics of helical fragments from mouse PrPC.
Dima RI, Thirumalai D.
Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15335-40
Pubmed
Emerging ideas on the molecular basis of protein and peptide aggregation.
Thirumalai D, Klimov DK, Dima RI.
Curr Opin Struct Biol. 2003 Apr;13(2):146-59
Pubmed
Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments.
Dima RI, Thirumalai D.
Biophys J. 2002 Sep;83(3):1268-80
Pubmed
Exploring protein aggregation and self-propagation using lattice models: phase diagram and kinetics.
Dima RI, Thirumalai D.
Protein Sci. 2002 May;11(5):1036-49
Pubmed
Protein threading by learning.
Chang I, Cieplak M, Dima RI, Maritan A, Banavar JR.
Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14350-5
Pubmed
Scoring functions in protein folding and design.
Dima RI, Banavar JR, Maritan A.
Protein Sci. 2000 Apr;9(4):812-9
Pubmed
Statistical mechanics of protein-like heteropolymers.
Dima RI, Banavar JR, Cieplak M, Maritan A.
Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):4904-7
Pubmed