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Papers authored by Shakhnovich EI

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Lethal mutagenesis in viruses and bacteria.

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Chen P and Shakhnovich EI

Genetics 183(2):639-50, 2009 Oct - Who cited this? | PubMed ID: 19620390 | Fulltext

Thymic selection of T-cell receptors as an extreme value problem.

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Kosmrlj A, Chakraborty AK, Kardar M, and Shakhnovich EI

Physical review letters 103(6):068103, 2009 Aug 7 - Who cited this? | PubMed ID: 19792616 | Fulltext

FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space.

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Kutchukian PS, Lou D, and Shakhnovich EI

Journal of chemical information and modeling 49(7):1630-42, 2009 Jul - Who cited this? | PubMed ID: 19527020 | Fulltext

DNA unzipping phase diagram calculated via replica theory.

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Roland CB, Hatch KA, Prentiss M, and Shakhnovich EI

Physical review. E, Statistical, nonlinear, and soft matter physics 79(5 Pt 1):051923, 2009 May - Who cited this? | PubMed ID: 19518496 | Fulltext

Slowly replicating lytic viruses: pseudolysogenic persistence and within-host competition.

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Zhang J and Shakhnovich EI

Physical review letters 102(17):178103, 2009 May 1 - Who cited this? | PubMed ID: 19518838 | Fulltext

All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples.

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Kutchukian PS, Yang JS, Verdine GL, and Shakhnovich EI

Journal of the American Chemical Society 131(13):4622-7, 2009 Apr 8 - Who cited this? | PubMed ID: 19334772 | Fulltext

Emergence of species in evolutionary "simulated annealing".

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Heo M, Kang L, and Shakhnovich EI

Proceedings of the National Academy of Sciences of the United States of America 106(6):1869-74, 2009 Feb 10 - Who cited this? | PubMed ID: 19164759 | Fulltext

SDR: a database of predicted specificity-determining residues in proteins.

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Donald JE and Shakhnovich EI

Nucleic acids research, 2008 Oct 16 - Who cited this? | PubMed ID: 18927118 | Fulltext

Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis.

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Faísca PF, Travasso RD, Ball RC, and Shakhnovich EI

The Journal of chemical physics 129(9):095108, 2008 Sep 7 - Who cited this? | PubMed ID: 19044896 | Fulltext

Improvisation in evolution of genes and genomes: whose structure is it anyway?.

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Shakhnovich BE and Shakhnovich EI

Current opinion in structural biology, 2008 May 17 - Who cited this? | PubMed ID: 18487041 | Fulltext

Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins.

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Pereira de Araújo AF, Gomes AL, Bursztyn AA, and Shakhnovich EI

Proteins 70(3):971, 2008 Feb 15 - Who cited this? | PubMed ID: 17847091 | Fulltext

Statistically enhanced promiscuity of structurally correlated patterns.

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Lukatsky DB and Shakhnovich EI

Physical review. E, Statistical, nonlinear, and soft matter physics 77(2 Pt 1):20901, 2008 Feb - Who cited this? | PubMed ID: 18351980 | Fulltext

Universality and diversity of folding mechanics for three-helix bundle proteins.

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Yang JS, Wallin S, and Shakhnovich EI

Proceedings of the National Academy of Sciences of the United States of America 105(3):895, 2008 Jan 22 - Who cited this? | PubMed ID: 18195374 | Fulltext

Understanding protein evolution: from protein physics to Darwinian selection.

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Zeldovich KB and Shakhnovich EI

Annual review of physical chemistry 59:105, 2008 - Who cited this? | PubMed ID: 17937598 | Fulltext

Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size.

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Zhang J, Maslov S, and Shakhnovich EI

Molecular systems biology 4:210, 2008 - Who cited this? | PubMed ID: 18682700 | Fulltext

Sensitivity-dependent model of protein-protein interaction networks.

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Zhang J and Shakhnovich EI

Physical biology 5(3):36011, 2008 - Who cited this? | PubMed ID: 18824789 | Fulltext

Protein stability imposes limits on organism complexity and speed of molecular evolution.

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Zeldovich KB, Chen P, and Shakhnovich EI

Proceedings of the National Academy of Sciences of the United States of America 104(41):16152, 2007 Oct 9 - Who cited this? | PubMed ID: 17913881 | Fulltext

Robust protein protein interactions in crowded cellular environments.

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Deeds EJ, Ashenberg O, Gerardin J, and Shakhnovich EI

Proceedings of the National Academy of Sciences of the United States of America 104(38):14952, 2007 Sep 18 - Who cited this? | PubMed ID: 17848524 | Fulltext

A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.

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Zeldovich KB, Chen P, Shakhnovich BE, and Shakhnovich EI

PLoS computational biology 3(7), 2007 Jul - Who cited this? | PubMed ID: 17630830 | Fulltext

Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations.

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Perlstein EO, Deeds EJ, Ashenberg O, Shakhnovich EI, and Schreiber SL

Proceedings of the National Academy of Sciences of the United States of America 104(25):10553, 2007 Jun 19 - Who cited this? | PubMed ID: 17566105 | Fulltext

The folding mechanics of a knotted protein.

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Wallin S, Zeldovich KB, and Shakhnovich EI

Journal of molecular biology 368(3):884, 2007 May 4 - Who cited this? | PubMed ID: 17368671 | Fulltext

Positive and negative design in stability and thermal adaptation of natural proteins.

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Berezovsky IN, Zeldovich KB, and Shakhnovich EI

PLoS computational biology 3(3), 2007 Mar 23 - Who cited this? | PubMed ID: 17381236 | Fulltext

A knowledge-based move set for protein folding.

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Chen WW, Yang JS, and Shakhnovich EI

Proteins 66(3):682, 2007 Feb 15 - Who cited this? | PubMed ID: 17143895 | Fulltext

Structural similarity enhances interaction propensity of proteins.

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Lukatsky DB, Shakhnovich BE, Mintseris J, and Shakhnovich EI

Journal of molecular biology 365(5):1596, 2007 Feb 2 - Who cited this? | PubMed ID: 17141268 | Fulltext

Divergent evolution of a structural proteome: phenomenological models.

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Roland CB and Shakhnovich EI

Biophysical journal 92(3):701, 2007 Feb 1 - Who cited this? | PubMed ID: 17071665 | Fulltext

Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions.

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Gomes AL, de Rezende JR, Pereira de Araújo AF, and Shakhnovich EI

Proteins 66(2):304, 2007 Feb 1 - Who cited this? | PubMed ID: 17109406 | Fulltext

Protein and DNA sequence determinants of thermophilic adaptation.

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Zeldovich KB, Berezovsky IN, and Shakhnovich EI

PLoS computational biology 3(1), 2007 Jan 12 - Who cited this? | PubMed ID: 17222055 | Fulltext

A structure-centric view of protein evolution, design, and adaptation.

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Deeds EJ and Shakhnovich EI

Advances in enzymology and related areas of molecular biology 75:133, 2007 - Who cited this? | PubMed ID: 17124867 | Fulltext

Energetics of protein-DNA interactions.

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Donald JE, Chen WW, and Shakhnovich EI

Nucleic acids research 35(4):1039, 2007 - Who cited this? | PubMed ID: 17259221 | Fulltext

All-atom ab initio folding of a diverse set of proteins.

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Yang JS, Chen WW, Skolnick J, and Shakhnovich EI

Structure (London, England : 1993) 15(1):53, 2007 Jan - Who cited this? | PubMed ID: 17223532 | Fulltext

Understanding ensemble protein folding at atomic detail.

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Hubner IA, Deeds EJ, and Shakhnovich EI

Proceedings of the National Academy of Sciences of the United States of America 103(47):17747, 2006 Nov 21 - Who cited this? | PubMed ID: 17095606 | Fulltext

Statistically enhanced self-attraction of random patterns.

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Lukatsky DB, Zeldovich KB, and Shakhnovich EI

Physical review letters 97(17):178101, 2006 Oct 27 - Who cited this? | PubMed ID: 17155509 | Fulltext

Semiconservative quasispecies equations for polysomic genomes: the haploid case.

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Tannenbaum E, Sherley JL, and Shakhnovich EI

Journal of theoretical biology 241(4):791, 2006 Aug 21 - Who cited this? | PubMed ID: 16527313 | Fulltext

Genetic instability and the quasispecies model.

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Brumer Y, Michor F, and Shakhnovich EI

Journal of theoretical biology 241(2):216, 2006 Jul 21 - Who cited this? | PubMed ID: 16386760 | Fulltext

Common motifs and topological effects in the protein folding transition state.

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Hubner IA, Lindberg M, Haglund E, Oliveberg M, and Shakhnovich EI

Journal of molecular biology 359(4):1075, 2006 Jun 16 - Who cited this? | PubMed ID: 16678203 | Fulltext

Physical origins of protein superfamilies.

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Zeldovich KB, Berezovsky IN, and Shakhnovich EI

Journal of molecular biology 357(4):1335, 2006 Apr 7 - Who cited this? | PubMed ID: 16483605 | Fulltext

Identification of the minimal protein-folding nucleus through loop-entropy perturbations.

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Lindberg MO, Haglund E, Hubner IA, Shakhnovich EI, and Oliveberg M

Proceedings of the National Academy of Sciences of the United States of America 103(11):4083, 2006 Mar 14 - Who cited this? | PubMed ID: 16505376 | Fulltext

Folding and binding: the conformational repertoire of proteins: folding, aggregation and structural recognition.

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Oliveberg M and Shakhnovich EI

Current opinion in structural biology 16(1):68, 2006 Feb - Who cited this? | PubMed ID: 16443362 | Fulltext

A simple physical model for scaling in protein-protein interaction networks.

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Deeds EJ, Ashenberg O, and Shakhnovich EI

Proceedings of the National Academy of Sciences of the United States of America 103(2):311, 2006 Jan 10 - Who cited this? | PubMed ID: 16384916 | Fulltext

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.

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von Grotthuss M, Plewczynski D, Ginalski K, Rychlewski L, and Shakhnovich EI

BMC bioinformatics 7:53, 2006 - Who cited this? | PubMed ID: 16460560 | Fulltext

High-resolution protein folding with a transferable potential.

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Hubner IA, Deeds EJ, and Shakhnovich EI

Proceedings of the National Academy of Sciences of the United States of America 102(52):18914, 2005 Dec 27 - Who cited this? | PubMed ID: 16365306 | Fulltext

Physics and evolution of thermophilic adaptation.

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Berezovsky IN and Shakhnovich EI

Proceedings of the National Academy of Sciences of the United States of America 102(36):12742, 2005 Sep 6 - Who cited this? | PubMed ID: 16120678 | Fulltext

Entropic stabilization of proteins and its proteomic consequences.

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Berezovsky IN, Chen WW, Choi PJ, and Shakhnovich EI

PLoS computational biology 1(4), 2005 Sep - Who cited this? | PubMed ID: 16201009 | Fulltext

Geometric and physical considerations for realistic protein models.

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Hubner IA and Shakhnovich EI

Physical review. E, Statistical, nonlinear, and soft matter physics 72(2 Pt 1):22901, 2005 Aug - Who cited this? | PubMed ID: 16196617 | Fulltext

Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations.

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Ding F, Guo W, Dokholyan NV, Shakhnovich EI, and Shea JE

Journal of molecular biology 350(5):1035, 2005 Jul 29 - Who cited this? | PubMed ID: 15982666 | Fulltext

Lessons from the design of a novel atomic potential for protein folding.

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Chen WW and Shakhnovich EI

Protein science : a publication of the Protein Society 14(7):1741, 2005 Jul - Who cited this? | PubMed ID: 15987903 | Fulltext

Nucleation and the transition state of the SH3 domain.

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Hubner IA, Edmonds KA, and Shakhnovich EI

Journal of molecular biology 349(2):424, 2005 Jun 3 - Who cited this? | PubMed ID: 15890206 | Fulltext

Determining functional specificity from protein sequences.

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Donald JE and Shakhnovich EI

Bioinformatics (Oxford, England) 21(11):2629, 2005 Jun 1 - Who cited this? | PubMed ID: 15797914 | Fulltext

The emergence of scaling in sequence-based physical models of protein evolution.

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Deeds EJ and Shakhnovich EI

Biophysical journal 88(6):3905, 2005 Jun - Who cited this? | PubMed ID: 15805176 | Fulltext

CoC: a database of universally conserved residues in protein folds.

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Donald JE, Hubner IA, Rotemberg VM, Shakhnovich EI, and Mirny LA

Bioinformatics (Oxford, England) 21(10):2539, 2005 May 15 - Who cited this? | PubMed ID: 15746286 | Fulltext

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