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Eric J. Deeds, Ph.D. - Publications

Affiliations: 
2005 Harvard University, Cambridge, MA, United States 
Area:
Protein Folding and Design, Molecular Evolution, Drug Discovery
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30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Vakser IA, Grudinin S, Jenkins NW, Kundrotas PJ, Deeds EJ. Docking-based long timescale simulation of cell-size protein systems at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America. 119: e2210249119. PMID 36191203 DOI: 10.1073/pnas.2210249119  0.369
2019 Vakser IA, Deeds EJ. Computational approaches to macromolecular interactions in the cell. Current Opinion in Structural Biology. 55: 59-65. PMID 30999240 DOI: 10.1016/J.Sbi.2019.03.012  0.395
2018 Suderman R, Deeds EJ. Intrinsic limits of information transmission in biochemical signalling motifs. Interface Focus. 8: 20180039. PMID 30443336 DOI: 10.1098/Rsfs.2018.0039  0.3
2017 Rowland MA, Greenbaum JM, Deeds EJ. Crosstalk and the evolvability of intracellular communication. Nature Communications. 8: 16009. PMID 28691706 DOI: 10.1038/Ncomms16009  0.331
2016 Nariya MK, Israeli J, Shi JJ, Deeds EJ. Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System. Plos Computational Biology. 12: e1004851. PMID 27078235 DOI: 10.1371/Journal.Pcbi.1004851  0.409
2015 Rowland MA, Harrison B, Deeds EJ. Phosphatase specificity and pathway insulation in signaling networks. Biophysical Journal. 108: 986-96. PMID 25692603 DOI: 10.1016/J.Bpj.2014.12.011  0.375
2015 Suderman R, Schauer A, Deeds EJ. Phenotypic Properties of Scaffold-Based Signaling Paradigms Biophysical Journal. 108: 614a. DOI: 10.1016/J.Bpj.2014.11.3341  0.375
2015 Briggs K, Deeds EJ. Optimizing the Assembly of Stacked Rings Biophysical Journal. 108: 220a-221a. DOI: 10.1016/J.Bpj.2014.11.1218  0.367
2014 Rowland MA, Deeds EJ. Crosstalk and the evolution of specificity in two-component signaling. Proceedings of the National Academy of Sciences of the United States of America. 111: 5550-5. PMID 24706803 DOI: 10.1073/Pnas.1317178111  0.313
2014 Deeds EJ, Rowland MA. The Evolution of Crosstalk in Signaling Networks Biophysical Journal. 106: 643a. DOI: 10.1016/J.Bpj.2013.11.3560  0.333
2013 Suderman R, Deeds EJ. Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of protein complexes. Plos Computational Biology. 9: e1003278. PMID 24130475 DOI: 10.1371/Journal.Pcbi.1003278  0.366
2013 Gowthaman R, Deeds EJ, Karanicolas J. Structural properties of non-traditional drug targets present new challenges for virtual screening. Journal of Chemical Information and Modeling. 53: 2073-81. PMID 23879197 DOI: 10.1021/Ci4002316  0.403
2012 Rowland MA, Fontana W, Deeds EJ. Crosstalk and competition in signaling networks. Biophysical Journal. 103: 2389-98. PMID 23283238 DOI: 10.1016/J.Bpj.2012.10.006  0.302
2012 Deeds EJ, Krivine J, Feret J, Danos V, Fontana W. Combinatorial complexity and compositional drift in protein interaction networks. Plos One. 7: e32032. PMID 22412851 DOI: 10.1371/Journal.Pone.0032032  0.432
2012 Deeds EJ, Bachman JA, Fontana W. Optimizing ring assembly reveals the strength of weak interactions. Proceedings of the National Academy of Sciences of the United States of America. 109: 2348-53. PMID 22308356 DOI: 10.1073/Pnas.1113095109  0.329
2011 Deeds EJ, Savage V, Fontana W. Curvature in metabolic scaling: a reply to MacKay. Journal of Theoretical Biology. 280: 197-8. PMID 21497609 DOI: 10.1016/J.Jtbi.2011.03.036  0.324
2008 Savage VM, Deeds EJ, Fontana W. Sizing up allometric scaling theory. Plos Computational Biology. 4: e1000171. PMID 18787686 DOI: 10.1371/Journal.Pcbi.1000171  0.358
2007 Deeds EJ, Ashenberg O, Gerardin J, Shakhnovich EI. Robust protein protein interactions in crowded cellular environments. Proceedings of the National Academy of Sciences of the United States of America. 104: 14952-7. PMID 17848524 DOI: 10.1073/Pnas.0702766104  0.546
2007 Perlstein EO, Deeds EJ, Ashenberg O, Shakhnovich EI, Schreiber SL. Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations. Proceedings of the National Academy of Sciences of the United States of America. 104: 10553-8. PMID 17566105 DOI: 10.1073/Pnas.0704037104  0.477
2007 Deeds EJ, Shakhnovich EI. A structure-centric view of protein evolution, design, and adaptation. Advances in Enzymology and Related Areas of Molecular Biology. 75: 133-91, xi-xii. PMID 17124867 DOI: 10.1002/9780471224464.Ch2  0.631
2006 Hubner IA, Deeds EJ, Shakhnovich EI. Understanding ensemble protein folding at atomic detail. Proceedings of the National Academy of Sciences of the United States of America. 103: 17747-52. PMID 17095606 DOI: 10.1073/Pnas.0605580103  0.707
2006 Deeds EJ, Ashenberg O, Shakhnovich EI. A simple physical model for scaling in protein-protein interaction networks. Proceedings of the National Academy of Sciences of the United States of America. 103: 311-6. PMID 16384916 DOI: 10.1073/Pnas.0509715102  0.594
2005 Hubner IA, Deeds EJ, Shakhnovich EI. High-resolution protein folding with a transferable potential. Proceedings of the National Academy of Sciences of the United States of America. 102: 18914-9. PMID 16365306 DOI: 10.1073/Pnas.0502181102  0.704
2005 Deeds EJ, Shakhnovich EI. The emergence of scaling in sequence-based physical models of protein evolution. Biophysical Journal. 88: 3905-11. PMID 15805176 DOI: 10.1529/Biophysj.104.051433  0.65
2005 Deeds EJ, Hennessey H, Shakhnovich EI. Prokaryotic phylogenies inferred from protein structural domains. Genome Research. 15: 393-402. PMID 15741510 DOI: 10.1101/Gr.3033805  0.595
2005 Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Research. 15: 385-92. PMID 15741509 DOI: 10.1101/Gr.3133605  0.553
2004 Tannenbaum E, Deeds EJ, Shakhnovich EI. Semiconservative replication in the quasispecies model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 061916. PMID 15244626 DOI: 10.1103/Physreve.69.061916  0.474
2004 Deeds EJ, Shakhnovich B, Shakhnovich EI. Proteomic traces of speciation. Journal of Molecular Biology. 336: 695-706. PMID 15095981 DOI: 10.1016/J.Jmb.2003.12.066  0.633
2003 Deeds EJ, Dokholyan NV, Shakhnovich EI. Protein evolution within a structural space. Biophysical Journal. 85: 2962-72. PMID 14581198 DOI: 10.1016/S0006-3495(03)74716-X  0.594
2003 Tannenbaum E, Deeds EJ, Shakhnovich EI. Equilibrium distribution of mutators in the single fitness peak model. Physical Review Letters. 91: 138105. PMID 14525341 DOI: 10.1103/Physrevlett.91.138105  0.49
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