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Items: 1 to 20 of 225


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.


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