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Margaret E. Johnson, Ph.D. - Publications

Biophysics Johns Hopkins University, Baltimore, MD 
Theoretical Biophysics

24 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
2020 Varga MJ, Fu Y, Loggia S, Yogurtcu ON, Johnson ME. NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale. Biophysical Journal. PMID 32470324 DOI: 10.1016/J.Bpj.2020.05.002  0.342
2020 Fu Y, Sodt AJ, Johnson ME. An Implicit Lipid Model for Efficient Reaction Diffusion Simulations of Proteins Binding to Arbitrary Surfaces Biophysical Journal. 118: 240a. DOI: 10.1016/J.Bpj.2019.11.1412  0.647
2019 Fu Y, Yogurtcu ON, Kothari R, Thorkelsdottir G, Sodt AJ, Johnson ME. An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology. The Journal of Chemical Physics. 151: 124115. PMID 31575182 DOI: 10.1063/1.5120516  0.652
2018 Johnson ME. Modeling the Self-Assembly of Protein Complexes through a Rigid-Body Rotational Reaction-Diffusion Algorithm. The Journal of Physical Chemistry. B. PMID 30256109 DOI: 10.1021/Acs.Jpcb.8B08339  0.342
2018 Holland DO, Johnson ME. Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis. Plos Computational Biology. 14: e1006022. PMID 29518071 DOI: 10.1371/Journal.Pcbi.1006022  0.367
2018 Yogurtcu ON, Johnson ME. Cytosolic proteins can exploit membrane localization to trigger functional assembly. Plos Computational Biology. 14: e1006031. PMID 29505559 DOI: 10.1371/Journal.Pcbi.1006031  0.348
2017 Holland DO, Shapiro BH, Xue P, Johnson ME. Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks. Scientific Reports. 7: 5631. PMID 28717235 DOI: 10.1038/S41598-017-05686-2  0.357
2015 Yogurtcu ON, Johnson ME. Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates. The Journal of Chemical Physics. 143: 084117. PMID 26328828 DOI: 10.1063/1.4929390  0.304
2014 Johnson ME, Hummer G. Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems. Physical Review. X. 4. PMID 26005592 DOI: 10.1103/Physrevx.4.031037  0.543
2014 Johnson ME, Hummer G. Heterogeneous Protein-Protein Interaction Systems Modeled using a New Integrator for Single-Particle Reaction Diffusion Biophysical Journal. 106: 378a. DOI: 10.1016/J.Bpj.2013.11.2139  0.568
2013 Johnson ME, Hummer G. Evolutionary pressure on the topology of protein interface interaction networks. The Journal of Physical Chemistry. B. 117: 13098-106. PMID 23701316 DOI: 10.1021/Jp402944E  0.538
2013 Johnson ME, Hummer G. Interface-resolved network of protein-protein interactions. Plos Computational Biology. 9: e1003065. PMID 23696724 DOI: 10.1371/Journal.Pcbi.1003065  0.552
2013 Johnson ME, Hummer G. The Topology of Interface Interaction Networks Reflects on Protein-Protein Interaction Specificity and Regulation Biophysical Journal. 104: 160a. DOI: 10.1016/J.Bpj.2012.11.903  0.548
2012 Johnson ME, Hummer G. Characterization of a dynamic string method for the construction of transition pathways in molecular reactions. The Journal of Physical Chemistry. B. 116: 8573-83. PMID 22616575 DOI: 10.1021/Jp212611K  0.523
2012 Johnson ME, Hummer G. Refining Protein Interaction Networks with Protein Structure and Kinetic Modeling Biophysical Journal. 102: 226a. DOI: 10.1016/J.Bpj.2011.11.1240  0.556
2011 Johnson ME, Hummer G. Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks. Proceedings of the National Academy of Sciences of the United States of America. 108: 603-8. PMID 21187424 DOI: 10.1016/J.Bpj.2010.12.378  0.551
2010 Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GN, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. The Journal of Physical Chemistry. B. 114: 2549-64. PMID 20136072 DOI: 10.1021/Jp910674D  0.712
2010 Johnson ME, Malardier-Jugroot C, Head-Gordon T. Effects of co-solvents on peptide hydration water structure and dynamics. Physical Chemistry Chemical Physics : Pccp. 12: 393-405. PMID 20023817 DOI: 10.1039/B915888J  0.76
2010 Malardier-Jugroot C, Bowron DT, Soper AK, Johnson ME, Head-Gordon T. Structure and water dynamics of aqueous peptide solutions in the presence of co-solvents. Physical Chemistry Chemical Physics : Pccp. 12: 382-92. PMID 20023816 DOI: 10.1039/B915346B  0.76
2009 Johnson ME, Head-Gordon T. Assessing thermodynamic-dynamic relationships for waterlike liquids. The Journal of Chemical Physics. 130: 214510. PMID 19508079 DOI: 10.1063/1.3140608  0.589
2009 Johnson ME, Malardier-Jugroot C, Murarka RK, Head-Gordon T. Hydration water dynamics near biological interfaces. The Journal of Physical Chemistry. B. 113: 4082-92. PMID 19425247 DOI: 10.1021/Jp806183V  0.739
2008 Malardier-Jugroot C, Johnson ME, Murarka RK, Head-Gordon T. Aqueous peptides as experimental models for hydration water dynamics near protein surfaces. Physical Chemistry Chemical Physics : Pccp. 10: 4903-8. PMID 18688534 DOI: 10.1039/B806995F  0.734
2007 Johnson ME, Head-Gordon T, Louis AA. Representability problems for coarse-grained water potentials. The Journal of Chemical Physics. 126: 144509. PMID 17444725 DOI: 10.1063/1.2715953  0.579
2006 Head-Gordon T, Johnson ME. Tetrahedral structure or chains for liquid water. Proceedings of the National Academy of Sciences of the United States of America. 103: 7973-7. PMID 16698934 DOI: 10.1073/Pnas.0510593103  0.554
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