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Items: 1 to 20 of 208


Evolutionary dynamics of viral escape under antibodies stress: A biophysical model.

Chéron N, Serohijos AW, Choi JM, Shakhnovich EI.

Protein Sci. 2016 Mar 3. doi: 10.1002/pro.2915. [Epub ahead of print]


Biophysical principles predict fitness landscapes of drug resistance.

Rodrigues JV, Bershtein S, Li A, Lozovsky ER, Hartl DL, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2016 Feb 29. pii: 201601441. [Epub ahead of print]


Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria.

Bershtein S, Serohijos AW, Bhattacharyya S, Manhart M, Choi JM, Mu W, Zhou J, Shakhnovich EI.

PLoS Genet. 2015 Oct 20;11(10):e1005612. doi: 10.1371/journal.pgen.1005612. eCollection 2015 Oct.


OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands.

Chéron N, Jasty N, Shakhnovich EI.

J Med Chem. 2015 Sep 23. [Epub ahead of print]


Repurposing of rutin for the inhibition of norovirus replication.

Chéron N, Yu C, Kolawole AO, Shakhnovich EI, Wobus CE.

Arch Virol. 2015 Sep;160(9):2353-8. doi: 10.1007/s00705-015-2495-y. Epub 2015 Jun 26.


Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences.

Tian J, Woodard JC, Whitney A, Shakhnovich EI.

PLoS Comput Biol. 2015 Apr 23;11(4):e1004207. doi: 10.1371/journal.pcbi.1004207. eCollection 2015 Apr.


Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding.

Choi JM, Serohijos AW, Murphy S, Lucarelli D, Lofranco LL, Feldman A, Shakhnovich EI.

Biophys J. 2015 Feb 17;108(4):795-8. doi: 10.1016/j.bpj.2015.01.001.


Is catalytic activity of chaperones a selectable trait for the emergence of heat shock response?

Çetinbaş M, Shakhnovich EI.

Biophys J. 2015 Jan 20;108(2):438-48. doi: 10.1016/j.bpj.2014.11.3468.


The influence of selection for protein stability on dN/dS estimations.

Dasmeh P, Serohijos AW, Kepp KP, Shakhnovich EI.

Genome Biol Evol. 2014 Oct 28;6(10):2956-67. doi: 10.1093/gbe/evu223.


Evolution of specificity in protein-protein interactions.

Peleg O, Choi JM, Shakhnovich EI.

Biophys J. 2014 Oct 7;107(7):1686-96. doi: 10.1016/j.bpj.2014.08.004.


Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics.

Serohijos AW, Shakhnovich EI.

Curr Opin Struct Biol. 2014 Jun;26:84-91. doi: 10.1016/ Epub 2014 Jun 19. Review.


A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior.

Estácio SG, Krobath H, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PF.

PLoS Comput Biol. 2014 May 8;10(5):e1003606. doi: 10.1371/journal.pcbi.1003606. eCollection 2014 May.


Influenza A H1N1 pandemic strain evolution--divergence and the potential for antigenic drift variants.

Klein EY, Serohijos AW, Choi JM, Shakhnovich EI, Pekosz A.

PLoS One. 2014 Apr 3;9(4):e93632. doi: 10.1371/journal.pone.0093632. eCollection 2014.


Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations.

Cetinbaş M, Shakhnovich EI.

PLoS Comput Biol. 2013;9(11):e1003269. doi: 10.1371/journal.pcbi.1003269. Epub 2013 Nov 7.


Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions.

Serohijos AW, Shakhnovich EI.

Mol Biol Evol. 2014 Jan;31(1):165-76. doi: 10.1093/molbev/mst189. Epub 2013 Oct 11.


Assessing the effect of loop mutations in the folding space of β2-microglobulin with molecular dynamics simulations.

Estácio SG, Shakhnovich EI, Faísca PF.

Int J Mol Sci. 2013 Aug 22;14(9):17256-78. doi: 10.3390/ijms140917256.


Structural and energetic determinants of co-translational folding.

Krobath H, Shakhnovich EI, Faísca PF.

J Chem Phys. 2013 Jun 7;138(21):215101. doi: 10.1063/1.4808044.


Positively selected sites in cetacean myoglobins contribute to protein stability.

Dasmeh P, Serohijos AW, Kepp KP, Shakhnovich EI.

PLoS Comput Biol. 2013;9(3):e1002929. doi: 10.1371/journal.pcbi.1002929. Epub 2013 Mar 7.


A one-shot germinal center model under protein structural stability constraints.

Raoof S, Heo M, Shakhnovich EI.

Phys Biol. 2013 Apr;10(2):025001. doi: 10.1088/1478-3975/10/2/025001. Epub 2013 Mar 15.


Highly abundant proteins favor more stable 3D structures in yeast.

Serohijos AW, Lee SY, Shakhnovich EI.

Biophys J. 2013 Feb 5;104(3):L1-3. doi: 10.1016/j.bpj.2012.11.3838.

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