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Items: 1 to 20 of 82

1.

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.

PMID:
29055297
2.

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 12. doi: 10.1021/jacs.7b07419. [Epub ahead of print]

PMID:
29019235
3.

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.

PMID:
28926712
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.

5.

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.

PMID:
28071910
6.

A MATHEMATICAL FRAMEWORK FOR EXACT MILESTONING.

Aristoff D, Bello-Rivas JM, Elber R.

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

7.

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.

8.

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.

9.

Perspective: Computer simulations of long time dynamics.

Elber R.

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

10.

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.

11.

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.

12.

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.

13.

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.

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.

15.

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.

16.

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.

17.

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.

18.

Exact milestoning.

Bello-Rivas JM, Elber R.

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

19.

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.

20.

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.

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