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ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory.

Wei W, Elber R.

J Chem Theory Comput. 2020 Jan 10. doi: 10.1021/acs.jctc.9b01030. [Epub ahead of print]


The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning.

Narayan B, Fathizadeh A, Templeton C, He P, Arasteh S, Elber R, Buchete NV, Levy RM.

Biochim Biophys Acta Gen Subj. 2019 Dec 27;1864(4):129508. doi: 10.1016/j.bbagen.2019.129508. [Epub ahead of print]


Defect-Assisted Permeation Through a Phospholipid Membrane: Experimental and Computational Study of the Peptide WKW.

Fathizadeh A, Kogan M, Anderson CM, Webb LJ, Elber R.

J Phys Chem B. 2019 Aug 8;123(31):6792-6798. doi: 10.1021/acs.jpcb.9b05414. Epub 2019 Jul 26.


Partition of Positively and Negatively Charged Tryptophan Ions in Membranes with Inverted Phospholipid Heads: Simulations and Experiments.

Cardenas AE, Anderson CM, Elber R, Webb LJ.

J Phys Chem B. 2019 Apr 18;123(15):3272-3281. doi: 10.1021/acs.jpcb.9b00754. Epub 2019 Apr 9.


Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations.

Chen YL, Lee T, Elber R, Pollack L.

Biophys J. 2019 Jan 8;116(1):19-30. doi: 10.1016/j.bpj.2018.11.020. Epub 2018 Nov 22.


Preferential Equilibrium Partitioning of Positively Charged Tryptophan into Phosphatidylcholine Bilayer Membranes.

Anderson CM, Cardenas A, Elber R, Webb LJ.

J Phys Chem B. 2019 Jan 10;123(1):170-179. doi: 10.1021/acs.jpcb.8b09872. Epub 2018 Dec 20.


Ion Permeation through a Phospholipid Membrane: Transition State, Path Splitting, and Calculation of Permeability.

Fathizadeh A, Elber R.

J Chem Theory Comput. 2019 Jan 8;15(1):720-730. doi: 10.1021/acs.jctc.8b00882. Epub 2018 Dec 7.


Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems.

Templeton C, Elber R.

J Am Chem Soc. 2018 Dec 12;140(49):16948-16951. doi: 10.1021/jacs.8b11111. Epub 2018 Nov 29.


Probing Translocation in Mutants of the Anthrax Channel: Atomically Detailed Simulations with Milestoning.

Ma P, Cardenas AE, Chaudhari MI, Elber R, Rempe SB.

J Phys Chem B. 2018 Nov 15;122(45):10296-10305. doi: 10.1021/acs.jpcb.8b08304. Epub 2018 Nov 5.


Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface.

Valentine ML, Cardenas AE, Elber R, Baiz CR.

Biophys J. 2018 Oct 16;115(8):1541-1551. doi: 10.1016/j.bpj.2018.08.044. Epub 2018 Sep 6.


Revealing the distinct folding phases of an RNA three-helix junction.

Plumridge A, Katz AM, Calvey GD, Elber R, Kirmizialtin S, Pollack L.

Nucleic Acids Res. 2018 Aug 21;46(14):7354-7365. doi: 10.1093/nar/gky363.


A new paradigm for atomically detailed simulations of kinetics in biophysical systems.

Elber R.

Q Rev Biophys. 2017 Jan;50:e8. doi: 10.1017/S0033583517000063. Review.


Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.

Templeton C, Chen SH, Fathizadeh A, Elber R.

J Chem Phys. 2017 Oct 21;147(15):152718. doi: 10.1063/1.4986298.


The Impact of Protonation on Early Translocation of Anthrax Lethal Factor: Kinetics from Molecular Dynamics Simulations and Milestoning Theory.

Ma P, Cardenas AE, Chaudhari MI, Elber R, Rempe SB.

J Am Chem Soc. 2017 Oct 25;139(42):14837-14840. doi: 10.1021/jacs.7b07419. Epub 2017 Oct 12.


Pyrophosphate Release in the Protein HIV Reverse Transcriptase.

Atis M, Johnson KA, Elber R.

J Phys Chem B. 2017 Oct 19;121(41):9557-9565. doi: 10.1021/acs.jpcb.7b08320. Epub 2017 Oct 4.


Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning.

Elber R, Bello-Rivas JM, Ma P, Cardenas AE, Fathizadeh A.

Entropy (Basel). 2017 May;19(5). pii: 219. doi: 10.3390/e19050219. Epub 2017 May 11.


Direct Measurement of the Effect of Cholesterol and 6-Ketocholestanol on the Membrane Dipole Electric Field Using Vibrational Stark Effect Spectroscopy Coupled with Molecular Dynamics Simulations.

Shrestha R, Anderson CM, Cardenas AE, Elber R, Webb LJ.

J Phys Chem B. 2017 Apr 20;121(15):3424-3436. doi: 10.1021/acs.jpcb.6b09007. Epub 2017 Jan 26.



Aristoff D, Bello-Rivas JM, Elber R.

Multiscale Model Simul. 2016;14(1):301-322. Epub 2016 Mar 3.


Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.

Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.


Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning.

Cardenas AE, Elber R.

J Phys Chem B. 2016 Aug 25;120(33):8208-16. doi: 10.1021/acs.jpcb.6b01890. Epub 2016 Apr 5.


Perspective: Computer simulations of long time dynamics.

Elber R.

J Chem Phys. 2016 Feb 14;144(6):060901. doi: 10.1063/1.4940794.


A Stochastic Algorithm for the Isobaric-Isothermal Ensemble with Ewald Summations for All Long Range Forces.

Di Pierro M, Elber R, Leimkuhler B.

J Chem Theory Comput. 2015 Dec 8;11(12):5624-37. doi: 10.1021/acs.jctc.5b00648. Epub 2015 Nov 25.


Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization.

Viswanath S, Dominguez L, Foster LS, Straub JE, Elber R.

Proteins. 2015 Dec;83(12):2170-85. doi: 10.1002/prot.24934. Epub 2015 Oct 14.


Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning.

Bello-Rivas JM, Elber R.

J Comput Chem. 2016 Mar 5;37(6):602-13. doi: 10.1002/jcc.24039. Epub 2015 Aug 12.


Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition.

Kirmizialtin S, Johnson KA, Elber R.

J Phys Chem B. 2015 Sep 3;119(35):11513-26. doi: 10.1021/acs.jpcb.5b05467. Epub 2015 Aug 14.


From an SNP to a Disease: A Comprehensive Statistical Analysis.

Elber R.

Structure. 2015 Jul 7;23(7):1155. doi: 10.1016/j.str.2015.06.005.


Comprehensive analysis of sequences of a protein switch.

Chen SH, Meller J, Elber R.

Protein Sci. 2016 Jan;25(1):135-46. doi: 10.1002/pro.2723. Epub 2015 Jul 1.


Membrane permeation of a peptide: it is better to be positive.

Cardenas AE, Shrestha R, Webb LJ, Elber R.

J Phys Chem B. 2015 May 28;119(21):6412-20. doi: 10.1021/acs.jpcb.5b02122. Epub 2015 May 13.


Molecular dynamics studies of modular polyketide synthase ketoreductase stereospecificity.

Mugnai ML, Shi Y, Keatinge-Clay AT, Elber R.

Biochemistry. 2015 Apr 14;54(14):2346-59. doi: 10.1021/bi501401g. Epub 2015 Apr 2.


Exact milestoning.

Bello-Rivas JM, Elber R.

J Chem Phys. 2015 Mar 7;142(9):094102. doi: 10.1063/1.4913399.


Measurement of the membrane dipole electric field in DMPC vesicles using vibrational shifts of p-cyanophenylalanine and molecular dynamics simulations.

Shrestha R, Cardenas AE, Elber R, Webb LJ.

J Phys Chem B. 2015 Feb 19;119(7):2869-76. doi: 10.1021/jp511677j. Epub 2015 Feb 4.


Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.

Mugnai ML, Elber R.

J Chem Phys. 2015 Jan 7;142(1):014105. doi: 10.1063/1.4904882.


Two is a pair, three is a network.

Elber R.

Biophys J. 2015 Jan 6;108(1):22. doi: 10.1016/j.bpj.2014.11.1855. No abstract available.


Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation.

Cardenas AE, Elber R.

J Chem Phys. 2014 Aug 7;141(5):054101. doi: 10.1063/1.4891305.


Optimizing potentials for a liquid mixture: a new force field for a tert-butanol and water solution.

Di Pierro M, Mugnai ML, Elber R.

J Phys Chem B. 2015 Jan 22;119(3):836-49. doi: 10.1021/jp505401m. Epub 2014 Aug 8.


DOCK/PIERR: web server for structure prediction of protein-protein complexes.

Viswanath S, Ravikant DV, Elber R.

Methods Mol Biol. 2014;1137:199-207. doi: 10.1007/978-1-4939-0366-5_14.


The energy landscape of a protein switch.

Chen SH, Elber R.

Phys Chem Chem Phys. 2014 Apr 14;16(14):6407-21. doi: 10.1039/c3cp55209h. Epub 2014 Jan 29.


Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples.

Viswanath S, Kreuzer SM, Cardenas AE, Elber R.

J Chem Phys. 2013 Nov 7;139(17):174105. doi: 10.1063/1.4827495.


Catch bond-like kinetics of helix cracking: network analysis by molecular dynamics and milestoning.

Kreuzer SM, Moon TJ, Elber R.

J Chem Phys. 2013 Sep 28;139(12):121902. doi: 10.1063/1.4811366. Erratum in: J Chem Phys. 2013 Oct 7;139(13):139901.


Coiled-coil response to mechanical force: global stability and local cracking.

Kreuzer SM, Elber R.

Biophys J. 2013 Aug 20;105(4):951-61. doi: 10.1016/j.bpj.2013.05.064.


Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model.

Meisburger SP, Sutton JL, Chen H, Pabit SA, Kirmizialtin S, Elber R, Pollack L.

Biopolymers. 2013 Dec;99(12):1032-45. doi: 10.1002/bip.22265.


Molecular machines.

Elber R, Kirmizialtin S.

Curr Opin Struct Biol. 2013 Apr;23(2):206-11. doi: 10.1016/ Epub 2013 Jan 8. Review.


Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization.

Ruymgaart AP, Elber R.

J Chem Theory Comput. 2012 Nov 13;8(11):4624-4636. Epub 2012 Aug 21.


Improving ranking of models for protein complexes with side chain modeling and atomic potentials.

Viswanath S, Ravikant DV, Elber R.

Proteins. 2013 Apr;81(4):592-606. doi: 10.1002/prot.24214. Epub 2012 Dec 24.


Thermodynamic Cycle Without Turning Off Self-Interactions: Formal Discussion and a Numerical Example.

Mugnai ML, Elber R.

J Chem Theory Comput. 2012;8(9):3022-3033. Epub 2012 Jul 25.


How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations.

Kirmizialtin S, Nguyen V, Johnson KA, Elber R.

Structure. 2012 Apr 4;20(4):618-27. doi: 10.1016/j.str.2012.02.018. Epub 2012 Apr 3.


Early events in helix unfolding under external forces: a milestoning analysis.

Kreuzer SM, Elber R, Moon TJ.

J Phys Chem B. 2012 Jul 26;116(29):8662-91. doi: 10.1021/jp300788e. Epub 2012 May 29.


The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations.

Kirmizialtin S, Silalahi AR, Elber R, Fenley MO.

Biophys J. 2012 Feb 22;102(4):829-38. doi: 10.1016/j.bpj.2011.12.055. Epub 2012 Feb 21.

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