Year |
Citation |
Score |
2022 |
Guo SK, Sodt AJ, Johnson ME. Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins. Plos Computational Biology. 18: e1009969. PMID 35312692 DOI: 10.1371/journal.pcbi.1009969 |
0.593 |
|
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 |
0.357 |
|
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 |
0.642 |
|
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 |
0.651 |
|
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 |
0.35 |
|
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 |
0.384 |
|
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 |
0.372 |
|
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 |
0.367 |
|
2017 |
Yogurtcu O, Johnson ME. Membrane Recruitment Enables Weak Binding Endocytic Proteins to Form Stable Complexes Biophysical Journal. 112: 91a. DOI: 10.1016/J.Bpj.2016.11.535 |
0.392 |
|
2017 |
Yogurtcu ON, Johnson ME. Membrane Recruitment can Increase the Number of Protein Assemblies by Many Folds: Insights from Theory and Reaction-Diffusion Simulation Biophysical Journal. 112: 46a. DOI: 10.1016/J.Bpj.2016.11.290 |
0.406 |
|
2016 |
Holland DO, Johnson ME. Optimizing Protein Specificity in the Crowded Cell through Concentration Balance and Network motif Selection Biophysical Journal. 110: 479a. DOI: 10.1016/J.Bpj.2015.11.2563 |
0.368 |
|
2016 |
Yogurtcu ON, Johnson ME. Governing Principles of Multiprotein Complex Formation on the Cell Membranes: An Investigation using Single-Molecule Resolution Spatio-Temporal Stochastic Computer Simulations and Analytical Calculations Biophysical Journal. 110: 347a. DOI: 10.1016/J.Bpj.2015.11.1866 |
0.396 |
|
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 |
0.307 |
|
2015 |
Calligari PA, Calandrini V, Ollivier J, Artero JB, Härtlein M, Johnson M, Kneller GR. Adaptation of Extremophilic Proteins with Temperature and Pressure: Evidence from Initiation Factor 6. The Journal of Physical Chemistry. B. 119: 7860-73. PMID 25996652 DOI: 10.1021/Acs.Jpcb.5B02034 |
0.303 |
|
2015 |
Yogurtcu ON, Johnson ME. Novel Single-Molecule Resolution Method for Spatio-Temporal Simulations of Protein Binding and Recruitment on the Membrane Biophysical Journal. 108: 526a. DOI: 10.1016/J.Bpj.2014.11.2883 |
0.433 |
|
2015 |
Holland DO, Johnson ME. Optimizing Protein Expression Levels as a Function of Network Topology Minimizes Nonfunctional Complex Formation Biophysical Journal. 108: 314a. DOI: 10.1016/J.Bpj.2014.11.1706 |
0.372 |
|
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 |
0.541 |
|
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 |
0.569 |
|
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 |
0.54 |
|
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 |
0.556 |
|
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 |
0.551 |
|
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 |
0.518 |
|
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 |
0.559 |
|
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 |
0.555 |
|
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 |
0.709 |
|
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 |
0.758 |
|
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 |
0.757 |
|
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 |
0.581 |
|
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 |
0.741 |
|
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 |
0.737 |
|
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 |
0.571 |
|
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 |
0.545 |
|
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