List of Publications | Research | Beckstein Lab

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List of Publications

List of Publications

List of publications of of the lab (since 2012) and Oliver Beckstein (2001–2011).

The list below is manually curated in Zotero and displayed with BibBaSE. For externally curated or automatically generated lists and other resources see external publication records.

  2017 (4)
Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library. Khoshlessan, M.; Paraskevakos, I.; Jha, S.; and Beckstein, O. In Huff, K.; Lippa, D.; Niederhut, D.; and Pacer, M, editor(s), Proceedings of the 16th Python in Science Conference, pages 64--72, Austin, TX, 2017.
Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library [link]Paper   doi   bibtex
Topological dissection of the membrane transport protein Mhp1 derived from cysteine accessibility and mass spectrometry. Calabrese, A. N.; Jackson, S. M.; Jones, L. N; Beckstein, O.; Heinkel, F.; Gsponer, J.; Sharples, D.; Sans, M.; Kokkinidou, M.; Pearson, A. R; Radford, S. E; Ashcroft, A. E; and Henderson, P. J. F. Analytical Chemistry, . July 2017.
Topological dissection of the membrane transport protein Mhp1 derived from cysteine accessibility and mass spectrometry [link]Paper   doi   bibtex   abstract
Ligandbook: an online repository for small and drug-like molecule force field parameters. Domański, J.; Beckstein, O.; and Iorga, B. I. Bioinformatics, 33(11): 1747--1749. June 2017.
Ligandbook: an online repository for small and drug-like molecule force field parameters [link]Paper   doi   bibtex
Structure of the SLC4 transporter Bor1p in an inward-facing conformation. Coudray, N.; Seyler, S. L.; Lasala, R.; Zhang, Z.; Clark, K. M.; Dumont, M. E.; Rohou, A.; Beckstein, O.; and Stokes, D. L. Protein Science, 26(1): 130--145. 2017.
doi   bibtex   abstract
  2016 (6)
Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters. Coincon, M.; Uzdavinys, P.; Nji, E.; Dotson, D. L.; Winkelmann, I.; Abdul-Hussein, S.; Cameron, A. D.; Beckstein, O.; and Drew, D. Nature Structural & Molecular Biology, 23(3): 248--255. March 2016.
Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters [link]Paper   doi   bibtex   abstract
Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field. Kenney, I. M.; Beckstein, O.; and Iorga, B. I. Journal of Computer-Aided Molecular Design, 30(11): 1045--1058. 2016.
doi   bibtex   abstract
Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA. Huang, Y.; Chen, W.; Dotson, D. L.; Beckstein, O.; and Shen, J. Nature Communications, 7: 12940. October 2016.
Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA [link]Paper   doi   bibtex   abstract
Datanet: CIF21 DIBBs: Middleware and High Performance Analytics Libraries for Scalable Data Science NSF14-43054 Progress Report. Geoffrey Charles Fox; Judy Qiu; David Crandall; Gregor von Laszewski; Shantenu Jha; Fusheng Wang; Madhav Marathe; John Paden; Tom Cheatham; and Oliver Beckstein . 2016.
Datanet: CIF21 DIBBs: Middleware and High Performance Analytics Libraries for Scalable Data Science NSF14-43054 Progress Report [link]Paper   doi   bibtex
datreant: persistent, Pythonic trees for heterogeneous data. Dotson, D. L.; Seyler, S. L; Linke, M.; Gowers, R. J.; and Beckstein, O. In Benthall, S.; and Rostrup, S., editor(s), Proceedings of the 15th Python in Science Conference, pages 51 -- 56, Austin, TX, 2016.
datreant: persistent, Pythonic trees for heterogeneous data [link]Paper   bibtex   abstract
MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. Gowers, R. J; Linke, M.; Barnoud, J.; T. J. E. Reddy; Melo, M. N.; Seyler, S. L.; Dotson, D. L.; Domanski, J.; Buchoux, S.; Kenney, I. M.; and Beckstein, O. In Benthall, S.; and Rostrup, S., editor(s), Proceedings of the 15th Python in Science Conference, pages 102--109, Austin, TX, 2016.
MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. [link]Paper   bibtex   abstract
  2015 (3)
Peptide Folding in Translocon-Like Pores. Ulmschneider, M. B.; Leman, J. K.; Fennell, H.; and Beckstein, O. The Journal of Membrane Biology, 248(3): 407--417. May 2015.
Peptide Folding in Translocon-Like Pores [link]Paper   doi   bibtex   abstract
Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. Seyler, S. L.; Kumar, A.; Thorpe, M. F.; and Beckstein, O. PLoS Comput Biol, 11(10): e1004568. October 2015.
Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways [link]Paper   doi   bibtex   abstract
Understanding Thermosensitive Transient Receptor Potential Channels as Versatile Polymodal Cellular Sensors. Hilton, J. K.; Rath, P.; Helsell, C. V. M.; Beckstein, O.; and Van Horn, W. D. Biochemistry, 54(15): 2401--2413. April 2015.
Understanding Thermosensitive Transient Receptor Potential Channels as Versatile Polymodal Cellular Sensors [link]Paper   doi   bibtex   abstract
  2014 (5)
Molecular mechanism of ligand recognition by a membrane transport protein, Mhp1. Simmons, K. J.; Jackson, S. M.; Brueckner, F.; Patching, S. G.; Beckstein, O.; Ivanova, E.; Geng, T.; Weyand, S.; Drew, D.; Lanigan, J.; Sharples, D. J.; Sansom, M. S.; Iwata, S.; Fishwick, C. W.; Johnson, A. P.; Cameron, A. D.; and Henderson, P. J. The EMBO Journal, 33: 1831--1844. June 2014.
Molecular mechanism of ligand recognition by a membrane transport protein, Mhp1 [link]Paper   doi   bibtex   abstract
Crystal structure of the sodium–proton antiporter NhaA dimer and new mechanistic insights. Lee, C.; Yashiro, S.; Dotson, D. L.; Uzdavinys, P.; Iwata, S.; Sansom, M. S. P.; Ballmoos, C. v.; Beckstein, O.; Drew, D.; and Cameron, A. D. The Journal of General Physiology, 144(6): 529--544. December 2014.
Crystal structure of the sodium–proton antiporter NhaA dimer and new mechanistic insights [link]Paper   doi   bibtex   abstract
Sampling large conformational transitions: adenylate kinase as a testing ground. Seyler, S. L.; and Beckstein, O. Molecular Simulation, 40(10-11): 855--877. 2014.
Sampling large conformational transitions: adenylate kinase as a testing ground [link]Paper   doi   bibtex   abstract
Prediction of hydration free energies for a diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field. Beckstein, O.; Fourrier, A.; and Iorga, B. I. J Comput Aided Mol Des, 28(3): 265--276. 2014.
Prediction of hydration free energies for a diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field [link]Paper   doi   bibtex   abstract
Flexible gates generate occluded intermediates in the transport cycle of LacY. Stelzl, L. S; Fowler, P. W; Sansom, M. S P; and Beckstein, O. J Mol Biol, 426: 735--751. 2014.
Flexible gates generate occluded intermediates in the transport cycle of LacY [link]Paper   doi   bibtex   abstract
  2013 (6)
The 5-helix inverted repeat superfamily of membrane transport proteins. Cameron, A. D; Beckstein, O.; and Henderson, P. J. In Roberts, G. C. K., editor(s), Encylopedia of Biophysics, pages 1481--1485. Springer, Berlin, Heidelberg, 2013.
The 5-helix inverted repeat superfamily of membrane transport proteins [link]Paper   bibtex   buy
Mhp1, the Na⁺-Hydantoin Membrane Transport Protein. Jackson, S. M; Ivanova, E.; Simmons, K.; Patching, S. G; Weyand, S.; Shimamura, T.; Brückner, F.; Iwata, S.; Sharples, D. J; Baldwin, S. A; Sansom, M. P.; Beckstein, O.; Cameron, A. D; and Henderson, P. J. In Roberts, G. C. K., editor(s), Encylopedia of Biophysics, pages 1514--1521. Springer, Berlin, Heidelberg, 2013.
Mhp1, the Na⁺-Hydantoin Membrane Transport Protein [link]Paper   bibtex   abstract   buy
Influence of lipids on protein-mediated transmembrane transport. Denning, E. J.; and Beckstein, O. Chem Phys Lipids, 169: 57--71. 2013.
Influence of lipids on protein-mediated transmembrane transport [link]Paper   doi   bibtex   abstract
A Detailed Examination of a Single Conduction Event in a Potassium Channel. Fowler, P. W.; Beckstein, O.; Abad, E.; and Sansom, M. S. P. J Phys Chem Lett, 4: 3104--3109. 2013.
A Detailed Examination of a Single Conduction Event in a Potassium Channel [link]Paper   doi   bibtex   abstract
A two-domain elevator mechanism for sodium/proton antiport. Lee, C.; Kang, H. J.; von Ballmoos, C.; Newstead, S.; Uzdavinys, P.; Dotson, D. L.; Iwata, S.; Beckstein, O.; Cameron, A. D.; and Drew, D. Nature, 501(7468): 573--577. 2013.
A two-domain elevator mechanism for sodium/proton antiport [link]Paper   doi   bibtex   abstract
Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels. Fowler, P. W.; Abad, E.; Beckstein, O.; and Sansom, M. S. P. Journal of Chemical Theory and Computation, 9(11): 5176--5189. 2013.
Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels [link]Paper   doi   bibtex   abstract
  2012 (4)
Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field. Beckstein, O.; and Iorga, B. I. J Comput Aided Mol Des, 26(5): 635--645. 2012.
Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field [link]Paper   doi   bibtex   abstract
Coarse grain simulations reveal movement of synaptobrevin C terminus in response to piconewton forces. Lindau, M.; Hall, B. A.; Chetwynd, A.; Beckstein, O.; and Sansom, M. S. P. Biophys J, 103: 959--969. 2012.
Coarse grain simulations reveal movement of synaptobrevin C terminus in response to piconewton forces [link]Paper   doi   bibtex   abstract
A novel congenital myasthenic syndrome due to decreased acetylcholine receptor ion channel conductance. Webster, R.; Maxwell, S.; Spearman, H.; Tai, K.; Beckstein, O.; Sansom, M.; and Beeson, D. Brain, 135(4): 1070--1080. 2012.
A novel congenital myasthenic syndrome due to decreased acetylcholine receptor ion channel conductance [link]Paper   doi   bibtex   abstract
Biomimetic Design of a Brush-Like Nanopore: Simulation Studies. Pongprayoon, P.; Beckstein, O.; and Sansom, M. S. P. J Phys Chem B, 116(1): 462--468. 2012.
Biomimetic Design of a Brush-Like Nanopore: Simulation Studies [link]Paper   doi   bibtex   abstract
  2011 (4)
The Nucleobase-Cation-Symport-1 Family of Membrane Transport Proteins. Weyand, S.; Ma, P.; Saidijam, M.; Baldwin, J.; Beckstein, O.; Jackson, S.; Suzuki, S.; Patching, S. G; Shimamura, T.; Sansom, M. S. P.; Iwata, S.; Cameron, A. D; Baldwin, S. A; and Henderson, P. J. F. In Messerschmidt, A., editor(s), Handbook of Metalloproteins, of Encyclopedia of Inorganic and Bioinorganic Chemistry. Wiley, 2011.
The Nucleobase-Cation-Symport-1 Family of Membrane Transport Proteins [link]Paper   bibtex   abstract   buy
MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. Michaud-Agrawal, N.; Denning, E. J.; Woolf, T. B.; and Beckstein, O. J Comp Chem, 32: 2319--2327. 2011.
MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations [link]Paper   doi   bibtex   abstract
Computing ensembles of transitions from stable states: Dynamic Importance Sampling. Perilla, J. R.; Beckstein, O.; Denning, E. J.; and Woolf, T. J Comp Chem, 32(2): 186--209. 2011.
Computing ensembles of transitions from stable states: Dynamic Importance Sampling [link]Paper   doi   bibtex   abstract
The alternating access mechanism of transport as observed in the sodium-hydantoin transporter Mhp1. Weyand, S.; Shimamura, T.; Beckstein, O.; Sansom, M. S. P.; Iwata, S.; Henderson, P. J. F.; and Cameron, A. D. J. Synchrotron Rad., 18(1): 20--23. 2011.
The alternating access mechanism of transport as observed in the sodium-hydantoin transporter Mhp1 [link]Paper   doi   bibtex   abstract
  2010 (2)
Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1. Shimamura, T.; Weyand, S.; Beckstein, O.; Rutherford, N. G; Hadden, J. M; Sharples, D.; Sansom, M. S P; Iwata, S.; Henderson, P. J F; and Cameron, A. D Science, 328(5977): 470--473. 2010.
Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1 [link]Paper   doi   bibtex   abstract
Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations. Domański, J.; Stansfeld, P.; Sansom, M.; and Beckstein, O. J Membr Biol, 236(3): 255--258. 2010.
Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations [link]Paper   doi   bibtex
  2009 (4)
New and Notable: Teaching old coefficients new tricks: new insight into the meaning of the osmotic and diffusive permeation coefficients. Beckstein, O. Biophys J, 96(3): 763--764. February 2009.
New and Notable: Teaching old coefficients new tricks: new insight into the meaning of the osmotic and diffusive permeation coefficients. [link]Paper   doi   bibtex
Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions. Beckstein, O.; Denning, E. J.; Perilla, J. R.; and Woolf, T. B. J Mol Biol, 394(1): 160--176. 2009.
Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions [link]Paper   doi   bibtex   abstract
Permeation of water through the KcsA K⁺ channel. Furini, S.; Beckstein, O.; and Domene, C. Proteins, 74(2): 437--448. 2009.
Permeation of water through the KcsA K⁺ channel. [link]Paper   doi   bibtex   abstract
Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate. Pongprayoon, P.; Beckstein, O.; Wee, C.; and Sansom, M. S. P. Proc Natl Acad Sci U S A, 106(51): 21614--21618. 2009.
Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate [link]Paper   doi   bibtex   abstract
  2008 (2)
Brownian Simulation of Charge Transport in α-Haemolysin. Millar, C.; Madathil, R.; Beckstein, O.; Sansom, M. S. P.; Roy, S.; and Asenov, A. Journal of Computational Electronics, 7(1): 28--33. March 2008.
Brownian Simulation of Charge Transport in α-Haemolysin [link]Paper   doi   bibtex   abstract
Opening a hydrophobic gate: the nicotinic acetylcholine receptor as an example. Rogers, S. E.; Tai, K.; Beckstein, O.; and Sansom, M. S. P. 2008. arXiv:0902.1417v1
Opening a hydrophobic gate: the nicotinic acetylcholine receptor as an example [link]Paper   bibtex
  2007 (1)
Continuum vs. particle simulations of model nano-pores. Millar, C.; Roy, S.; Beckstein, O.; Sansom, M.; and Asenov, A. Journal of Computational Electronics, 6(1): 367--371. 2007.
Continuum vs. particle simulations of model nano-pores [link]Paper   doi   bibtex   abstract
  2006 (1)
A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor. Beckstein, O.; and Sansom, M. S. P. Physical Biology, 3(2): 147--159. 2006.
A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor [link]Paper   doi   bibtex   abstract
  2005 (2)
Principles of Gating Mechanisms of Ion Channels. Beckstein, O. Ph.D. Thesis, University of Oxford, Oxford, UK, 2005.
Principles of Gating Mechanisms of Ion Channels [link]Paper   bibtex   abstract
The alpha7 nicotinic acetylcholine receptor: Molecular modelling, electrostatics and energetics of permeation. Amiri, S.; Tai, K.; Beckstein, O.; Biggin, P. C.; and Sansom, M. S. P. Mol Mem Biol, 22: 151--162. 2005.
The alpha7 nicotinic acetylcholine receptor: Molecular modelling, electrostatics and energetics of permeation [link]Paper   doi   bibtex   abstract
  2004 (2)
The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores. Beckstein, O.; and Sansom, M. S. P. Physical Biology, 1(1): 42--52. 2004.
The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores [link]Paper   doi   bibtex   abstract
Not ions alone: Barriers to Ion Permeation in Nanopores and Channels. Beckstein, O.; Tai, K.; and Sansom, M. S. P. J Am Chem Soc, 126(45): 14694--14695. 2004.
Not ions alone: Barriers to Ion Permeation in Nanopores and Channels [link]Paper   doi   bibtex   abstract
  2003 (2)
Liquid-vapor oscillations of water in hydrophobic nanopores. Beckstein, O.; and Sansom, M. S. P. Proc Natl Acad Sci U S A, 100: 7063--7068. 2003.
Liquid-vapor oscillations of water in hydrophobic nanopores [link]Paper   doi   bibtex   abstract
Ion channel gating: insights via molecular simulations. Beckstein, O.; Biggin, P. C.; Bond, P.; Bright, J. N.; Domene, C.; Grottesi, A.; Holyoake, J.; and Sansom, M. S. P. FEBS Lett, 555: 85--90. 2003.
Ion channel gating: insights via molecular simulations [link]Paper   bibtex
  2002 (1)
Water in ion channels and pores—simulation studies. Sansom, M. S. P.; Bond, P.; Beckstein, O.; Biggin, P. C.; Faraldo-Goméz, J.; Law, R. J.; Patargias, G.; and Tieleman, D. P. In Bock, G.; and Goode, J. A., editor(s), Ion channels: from atomic resolution physiology to functional genomics, volume 245, of Novartis Foundation Symposia, pages 66--78, 2002. John Wiley & Sons, Chicester
Water in ion channels and pores—simulation studies [link]Paper   doi   bibtex
  2001 (4)
Elastic Constants How-To. Beckstein, O. Technical Report Universität Erlangen-Nürnberg, Erlangen, 2001.
Elastic Constants How-To [link]Paper   bibtex   abstract
Chemical bonding, elasticity, and valence force field models: A case study for α-Pt₂Si and PtSi. Klepeis, J. E.; Beckstein, O.; Pankratov, O.; and Hart, G. L. W. Phys Rev B, 64(15): 155110. 2001.
Chemical bonding, elasticity, and valence force field models: A case study for α-Pt₂Si and PtSi [link]Paper   doi   bibtex
First-principles elastic constants and electronic structure of α-Pt₂Si and PtSi. Beckstein, O.; Klepeis, J. E.; Hart, G. L. W.; and Pankratov, O. Phys Rev B, 63(13): 134112. 2001.
First-principles elastic constants and electronic structure of α-Pt₂Si and PtSi [link]Paper   doi   bibtex
A Hydrophobic Gating Mechanism for Nanopores. Beckstein, O.; Biggin, P. C.; and Sansom, M. S. P. J Phys Chem B, 105(51): 12902--12905. December 2001.
A Hydrophobic Gating Mechanism for Nanopores [link]Paper   doi   bibtex   abstract
  1999 (1)
Strukturelle und elektronische Eigenschaften der Platinsilizide aus ab initio Rechnungen. Beckstein, O. Ph.D. Thesis, Universität Erlangen-Nürnberg, Erlangen, Germany, 1999.
Strukturelle und elektronische Eigenschaften der Platinsilizide aus ab initio Rechnungen [link]Paper   bibtex   abstract
  1993 (1)
The pH dependence of the apparent equilibrium constant, K′, of a biochemical reaction. Alberty, R. A.; and Cornish-Bowden, A. Trends in Biochemical Sciences, 18(8): 288 -- 291. 1993.
The pH dependence of the apparent equilibrium constant, K′, of a biochemical reaction [link]Paper   doi   bibtex   abstract

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