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Joshua L. Adelman, Ph.D. - Publications

Affiliations: 
University of California, Berkeley, Berkeley, CA, United States 
Area:
protein motors, eukaryotic and prokaryotic cell motility, membrane geometry and protein organization and pattern formation in neural systems
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27 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
2023 Bogetti AT, Leung JMG, Russo JD, Zhang S, Thompson JP, Saglam AS, Ray D, Mostofian B, Pratt AJ, Abraham RC, Harrison PO, Dudek M, Torrillo PA, DeGrave AJ, Adhikari U, ... ... Adelman JL, et al. A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]. Living Journal of Computational Molecular Science. 5. PMID 37200895 DOI: 10.33011/livecoms.5.1.1655  0.762
2022 Russo JD, Zhang S, Leung JMG, Bogetti AT, Thompson JP, DeGrave AJ, Torrillo PA, Pratt AJ, Wong KF, Xia J, Copperman J, Adelman JL, Zwier MC, LeBard DN, Zuckerman DM, et al. WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications. Journal of Chemical Theory and Computation. PMID 35043623 DOI: 10.1021/acs.jctc.1c01154  0.755
2019 Bogetti AT, Mostofian B, Dickson A, Pratt AJ, Saglam AS, Harrison PO, Adelman JL, Dudek M, Torrillo PA, DeGrave AJ, Adhikari U, Zwier MC, Zuckerman DM, Chong LT. A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]. Living Journal of Computational Molecular Science. 1. PMID 32395705 DOI: 10.33011/livecoms.1.2.10607  0.76
2017 Capponi S, Adelman J, Rosenberg J, Grabe M. Weighted Ensemble Approach to In Silico Measure the I-V Relationship in a K + Ion Channel Biophysical Journal. 112: 543a. DOI: 10.1016/J.Bpj.2016.11.2933  0.64
2017 Suárez E, Adelman JL, Zuckerman DM. Mechanism Beyond Markov Models: History Information is Needed for Unbiased Pathway Reconstruction of Protein Folding Biophysical Journal. 112: 289a-290a. DOI: 10.1016/J.Bpj.2016.11.1569  0.644
2016 Zwier MC, Pratt A, Adelman JL, Kaus JW, Zuckerman DM, Chong LT. Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide. The Journal of Physical Chemistry Letters. PMID 27532687 DOI: 10.1021/Acs.Jpclett.6B01502  0.749
2016 Suárez E, Adelman JL, Zuckerman DM. Accurate estimation of protein folding and unfolding times: Beyond Markov state models. Journal of Chemical Theory and Computation. PMID 27340835 DOI: 10.1021/Acs.Jctc.6B00339  0.622
2016 Adelman JL, Ghezzi C, Bisignano P, Loo DD, Choe S, Abramson J, Rosenberg JM, Wright EM, Grabe M. Stochastic steps in secondary active sugar transport. Proceedings of the National Academy of Sciences of the United States of America. PMID 27325773 DOI: 10.1073/Pnas.1525378113  0.697
2015 Adelman JL, Grabe M. Simulating current-voltage relationships for a narrow ion channel using the weighted ensemble method. Journal of Chemical Theory and Computation. 11: 1907-1918. PMID 26392816 DOI: 10.1021/Ct501134S  0.716
2015 Zwier MC, Adelman JL, Kaus JW, Pratt AJ, Wong KF, Rego NB, Suárez E, Lettieri S, Wang DW, Grabe M, Zuckerman DM, Chong LT. WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis. Journal of Chemical Theory and Computation. 11: 800-809. PMID 26392815 DOI: 10.1021/Ct5010615  0.78
2015 Buck TM, Jordan R, Lyons-Weiler J, Adelman JL, Needham PG, Kleyman TR, Brodsky JL. Expression of three topologically distinct membrane proteins elicits unique stress response pathways in the yeast Saccharomyces cerevisiae. Physiological Genomics. 47: 198-214. PMID 25759377 DOI: 10.1152/Physiolgenomics.00101.2014  0.314
2015 Zwier MC, Adelman JL, Kaus JW, Pratt AJ, Wong KF, Rego NB, Suárez E, Lettieri S, Wang DW, Grabe M, Zuckerman DM, Chong LT. WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis Journal of Chemical Theory and Computation. 11: 800-809. DOI: 10.1021/ct5010615  0.763
2014 Choudhary OP, Paz A, Adelman JL, Colletier JP, Abramson J, Grabe M. Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1. Nature Structural & Molecular Biology. 21: 626-32. PMID 24908397 DOI: 10.1038/Nsmb.2841  0.771
2014 Adelman JL, Sheng Y, Choe S, Abramson J, Wright EM, Rosenberg JM, Grabe M. Structural determinants of water permeation through the sodium-galactose transporter vSGLT. Biophysical Journal. 106: 1280-9. PMID 24655503 DOI: 10.1016/J.Bpj.2014.01.006  0.703
2014 Choudhary OP, Paz A, Adelman J, Colletier J, Abramson J, Grabe M. Characterizing ATP Permeation through the Voltage-Dependent Anion Channel VDAC Biophysical Journal. 106: 147a-148a. DOI: 10.1016/J.Bpj.2013.11.851  0.751
2014 Adelman JL, Grabe M. Simulating Current-Voltage Relationships for a Simple Ion Channel with All-Atom Resolution using the Weighted Ensemble Method Biophysical Journal. 106: 805a. DOI: 10.1016/J.Bpj.2013.11.4411  0.697
2014 Pendse P, Choe S, Adelman J, Abramson J, Wright E, Rosenberg J, Grabe M. Energetics of Urea Permeation through Sodium-Dependent Galactose Cotransporter vSGLT Biophysical Journal. 106: 365a. DOI: 10.1016/J.Bpj.2013.11.2072  0.722
2014 Adelman JL, Sheng Y, Choe S, Abramson J, Wright EM, Grabe M. Insight into the Mechanism of Water Permeation through the Sodium-Galactose Transporter vSGLT from Long Molecular Dynamics Simulations Biophysical Journal. 106: 365a. DOI: 10.1016/J.Bpj.2013.11.2071  0.697
2013 Adelman JL, Grabe M. Simulating rare events using a weighted ensemble-based string method. The Journal of Chemical Physics. 138: 044105. PMID 23387566 DOI: 10.1063/1.4773892  0.682
2013 Adelman JL, Grabe M. Efficient Simulation of Complex Transition Pathways using a Weighted Ensemble Based String Method Biophysical Journal. 104: 504a. DOI: 10.1016/J.Bpj.2012.11.2781  0.709
2012 Adelman JL, Dale AL, Zwier MC, Bhatt D, Chong LT, Zuckerman DM, Grabe M. Insight into the Alternating Access Mechanism of the Sodium Symporter Mhp1 using Path Sampling Simulations Biophysical Journal. 102: 661a-662a. DOI: 10.1016/J.Bpj.2011.11.3604  0.79
2012 Choe S, Adelman JL, Rosenberg JM, Wright EM, Abramson J, Grabe M. Understanding Substrate Unbinding from the Sodium-Galactose Co-Transporter vSGLT based on 16 Microseconds of Molecular Simulation Biophysical Journal. 102: 661a. DOI: 10.1016/J.Bpj.2011.11.3603  0.72
2012 Choudhary OP, Adelman J, Abramson J, Grabe M. Characterizing ATP Permeation through mVDAC1 using Markov State Models (MSMs) Biophysical Journal. 102: 550a. DOI: 10.1016/J.Bpj.2011.11.3002  0.752
2011 Adelman JL, Dale AL, Zwier MC, Bhatt D, Chong LT, Zuckerman DM, Grabe M. Simulations of the alternating access mechanism of the sodium symporter Mhp1. Biophysical Journal. 101: 2399-407. PMID 22098738 DOI: 10.1016/J.Bpj.2011.09.061  0.783
2011 Kashlan OB, Adelman JL, Okumura S, Blobner BM, Zuzek Z, Hughey RP, Kleyman TR, Grabe M. Constraint-based, homology model of the extracellular domain of the epithelial Na+ channel α subunit reveals a mechanism of channel activation by proteases. The Journal of Biological Chemistry. 286: 649-60. PMID 20974852 DOI: 10.1074/Jbc.M110.167098  0.674
2010 Adelman JL, Chodera JD, Kuo IF, Miller TF, Barsky D. The mechanical properties of PCNA: implications for the loading and function of a DNA sliding clamp. Biophysical Journal. 98: 3062-9. PMID 20550919 DOI: 10.1016/J.Bpj.2010.03.056  0.356
2006 Adelman JL, Jeong YJ, Liao JC, Patel G, Kim DE, Oster G, Patel SS. Mechanochemistry of transcription termination factor Rho. Molecular Cell. 22: 611-21. PMID 16762834 DOI: 10.1016/J.Molcel.2006.04.022  0.716
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