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ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.

Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI.

Bioinformatics. 2018 Jul 13. doi: 10.1093/bioinformatics/bty516. [Epub ahead of print] No abstract available.


Evolution on the biophysical fitness landscape of an RNA virus.

Rotem A, Serohijos AWR, Chang CB, Wolfe JT, Fischer AE, Mehoke TS, Zhang H, Tao Y, Ung WL, Choi JM, Rodrigues JV, Abimbola OK, Koehler SA, Wu S, Thielen PM, Cui N, Demirev PA, Giacobbi NS, Julian TR, Schwab K, Lin JS, Smith TJ, Pipas JM, Wobus CE, Feldman AB, Weitz DA, Shakhnovich EI.

Mol Biol Evol. 2018 Jun 28. doi: 10.1093/molbev/msy131. [Epub ahead of print]


Accessibility of the Shine-Dalgarno Sequence Dictates N-Terminal Codon Bias in E. coli.

Bhattacharyya S, Jacobs WM, Adkar BV, Yan J, Zhang W, Shakhnovich EI.

Mol Cell. 2018 Jun 7;70(5):894-905.e5. doi: 10.1016/j.molcel.2018.05.008. Epub 2018 Jun 7.


ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.

Razban RM, Gilson AI, Durfee N, Strobelt H, Dinkla K, Choi JM, Pfister H, Shakhnovich EI.

Bioinformatics. 2018 May 8. doi: 10.1093/bioinformatics/bty370. [Epub ahead of print]


Trade-offs between microbial growth phases lead to frequency-dependent and non-transitive selection.

Manhart M, Adkar BV, Shakhnovich EI.

Proc Biol Sci. 2018 Feb 14;285(1872). pii: 20172459. doi: 10.1098/rspb.2017.2459.


Absence of Selection for Quantum Coherence in the Fenna-Matthews-Olson Complex: A Combined Evolutionary and Excitonic Study.

Valleau S, Studer RA, Häse F, Kreisbeck C, Saer RG, Blankenship RE, Shakhnovich EI, Aspuru-Guzik A.

ACS Cent Sci. 2017 Oct 25;3(10):1086-1095. doi: 10.1021/acscentsci.7b00269. Epub 2017 Aug 30.


Evidence of evolutionary selection for cotranslational folding.

Jacobs WM, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11434-11439. doi: 10.1073/pnas.1705772114. Epub 2017 Oct 10.


Optimization of lag phase shapes the evolution of a bacterial enzyme.

Adkar BV, Manhart M, Bhattacharyya S, Tian J, Musharbash M, Shakhnovich EI.

Nat Ecol Evol. 2017 Apr 28;1(6):149. doi: 10.1038/s41559-017-0149.


A tale of two tails: The importance of unstructured termini in the aggregation pathway of β2-microglobulin.

Loureiro RJS, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, Faísca PFN.

Proteins. 2017 Nov;85(11):2045-2057. doi: 10.1002/prot.25358. Epub 2017 Aug 8.


Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations.

Chéron N, Shakhnovich EI.

J Comput Chem. 2017 Aug 15;38(22):1941-1951. doi: 10.1002/jcc.24839. Epub 2017 Jun 1.


The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution.

Gilson AI, Marshall-Christensen A, Choi JM, Shakhnovich EI.

Biophys J. 2017 Apr 11;112(7):1350-1365. doi: 10.1016/j.bpj.2017.02.029.


Graph's Topology and Free Energy of a Spin Model on the Graph.

Choi JM, Gilson AI, Shakhnovich EI.

Phys Rev Lett. 2017 Feb 24;118(8):088302. doi: 10.1103/PhysRevLett.118.088302. Epub 2017 Feb 24.


A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016.

Debroise T, Shakhnovich EI, Chéron N.

J Chem Inf Model. 2017 Mar 27;57(3):584-593. doi: 10.1021/acs.jcim.6b00610. Epub 2017 Feb 27.


Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity.

Bhattacharyya S, Bershtein S, Yan J, Argun T, Gilson AI, Trauger SA, Shakhnovich EI.

Elife. 2016 Dec 10;5. pii: e20309. doi: 10.7554/eLife.20309.


Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

Bershtein S, Serohijos AW, Shakhnovich EI.

Curr Opin Struct Biol. 2017 Feb;42:31-40. doi: 10.1016/ Epub 2016 Oct 31. Review.


Structure-Based Prediction of Protein-Folding Transition Paths.

Jacobs WM, Shakhnovich EI.

Biophys J. 2016 Sep 6;111(5):925-36. doi: 10.1016/j.bpj.2016.06.031.


An Internal Disulfide Locks a Misfolded Aggregation-prone Intermediate in Cataract-linked Mutants of Human γD-Crystallin.

Serebryany E, Woodard JC, Adkar BV, Shabab M, King JA, Shakhnovich EI.

J Biol Chem. 2016 Sep 2;291(36):19172-83. doi: 10.1074/jbc.M116.735977. Epub 2016 Jul 14.


A Simple Model of Protein Domain Swapping in Crowded Cellular Environments.

Woodard JC, Dunatunga S, Shakhnovich EI.

Biophys J. 2016 Jun 7;110(11):2367-2376. doi: 10.1016/j.bpj.2016.04.033.


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

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

Protein Sci. 2016 Jul;25(7):1332-40. doi: 10.1002/pro.2915. Epub 2016 Mar 24.


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 Mar 15;113(11):E1470-8. doi: 10.1073/pnas.1601441113. Epub 2016 Feb 29. Erratum in: Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):E1964.


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. 2016 May 12;59(9):4171-88. doi: 10.1021/acs.jmedchem.5b00886. Epub 2015 Sep 23.


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 AWR, Murphy S, Lucarelli D, Lofranco LL, Feldman A, Shakhnovich EI.

Biophys J. 2015 Feb 17;108(4):795-798. 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.


Gene Dosage Experiments in Enterobacteriaceae Using Arabinose-regulated Promoters.

Bhattacharyya S, Bershtein S, Shakhnovich EI.

Bio Protoc. 2014 Jul 20;7(14). pii: e2396. doi: 10.21769/BioProtoc.2396.


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.


A universal trend among proteomes indicates an oily last common ancestor.

Mannige RV, Brooks CL, Shakhnovich EI.

PLoS Comput Biol. 2012;8(12):e1002839. doi: 10.1371/journal.pcbi.1002839. Epub 2012 Dec 27.


Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness.

Bershtein S, Mu W, Serohijos AW, Zhou J, Shakhnovich EI.

Mol Cell. 2013 Jan 10;49(1):133-44. doi: 10.1016/j.molcel.2012.11.004. Epub 2012 Dec 6.


Collapse of unfolded proteins in a mixture of denaturants.

Xia Z, Das P, Shakhnovich EI, Zhou R.

J Am Chem Soc. 2012 Nov 7;134(44):18266-74. doi: 10.1021/ja3031505. Epub 2012 Oct 24.


Protein biophysics explains why highly abundant proteins evolve slowly.

Serohijos AW, Rimas Z, Shakhnovich EI.

Cell Rep. 2012 Aug 30;2(2):249-56. doi: 10.1016/j.celrep.2012.06.022. Epub 2012 Aug 2.


Robustness of atomistic Gō models in predicting native-like folding intermediates.

Estácio SG, Fernandes CS, Krobath H, Faísca PF, Shakhnovich EI.

J Chem Phys. 2012 Aug 28;137(8):085102.


Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation.

Wylie CS, Shakhnovich EI.

PLoS Comput Biol. 2012;8(8):e1002609. doi: 10.1371/journal.pcbi.1002609. Epub 2012 Aug 2.


Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants.

Krobath H, Estácio SG, Faísca PFN, Shakhnovich EI.

J Mol Biol. 2012 Oct 5;422(5):705-722. doi: 10.1016/j.jmb.2012.06.020. Epub 2012 Jun 20.


Is there an en route folding intermediate for Cold shock proteins?

Huang L, Shakhnovich EI.

Protein Sci. 2012 May;21(5):677-85. doi: 10.1002/pro.2053. Epub 2012 Mar 29.


Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations.

Bershtein S, Mu W, Shakhnovich EI.

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4857-62. doi: 10.1073/pnas.1118157109. Epub 2012 Mar 12. Erratum in: Proc Natl Acad Sci U S A. 2012 May 1;109(18):7126. Wu, Wanmeng [corrected to Mu, Wanmeng].


Sequence correlations shape protein promiscuity.

Lukatsky DB, Afek A, Shakhnovich EI.

J Chem Phys. 2011 Aug 14;135(6):065104. doi: 10.1063/1.3624332.


Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations.

Nivón LG, Shakhnovich EI.

J Mol Biol. 2011 Sep 2;411(5):1128-44. doi: 10.1016/j.jmb.2011.06.042. Epub 2011 Jun 30.

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