Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 101

1.

Efficient sampling of puckering states of monosaccharides through replica exchange with solute tempering and bond softening.

Wang L, Berne BJ.

J Chem Phys. 2018 Aug 21;149(7):072306. doi: 10.1063/1.5024389.

PMID:
30134707
2.

Predicting reaction coordinates in energy landscapes with diffusion anisotropy.

Tiwary P, Berne BJ.

J Chem Phys. 2017 Oct 21;147(15):152701. doi: 10.1063/1.4983727.

3.

Advancing Drug Discovery through Enhanced Free Energy Calculations.

Abel R, Wang L, Harder ED, Berne BJ, Friesner RA.

Acc Chem Res. 2017 Jul 18;50(7):1625-1632. doi: 10.1021/acs.accounts.7b00083. Epub 2017 Jul 5.

PMID:
28677954
4.

How and when does an anticancer drug leave its binding site?

Tiwary P, Mondal J, Berne BJ.

Sci Adv. 2017 May 31;3(5):e1700014. doi: 10.1126/sciadv.1700014. eCollection 2017 May.

5.

Simulated Force Quench Dynamics Shows GB1 Protein Is Not a Two State Folder.

Berkovich R, Mondal J, Paster I, Berne BJ.

J Phys Chem B. 2017 May 25;121(20):5162-5173. doi: 10.1021/acs.jpcb.7b00610. Epub 2017 May 11.

PMID:
28453938
6.

Nitriles at Silica Interfaces Resemble Supported Lipid Bilayers.

Berne BJ, Fourkas JT, Walker RA, Weeks JD.

Acc Chem Res. 2016 Sep 20;49(9):1605-13. doi: 10.1021/acs.accounts.6b00169. Epub 2016 Aug 15.

7.

How wet should be the reaction coordinate for ligand unbinding?

Tiwary P, Berne BJ.

J Chem Phys. 2016 Aug 7;145(5):054113. doi: 10.1063/1.4959969.

8.

Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations.

Clark AJ, Tiwary P, Borrelli K, Feng S, Miller EB, Abel R, Friesner RA, Berne BJ.

J Chem Theory Comput. 2016 Jun 14;12(6):2990-8. doi: 10.1021/acs.jctc.6b00201. Epub 2016 May 13.

PMID:
27145262
9.

Kramers turnover: From energy diffusion to spatial diffusion using metadynamics.

Tiwary P, Berne BJ.

J Chem Phys. 2016 Apr 7;144(13):134103. doi: 10.1063/1.4944577.

10.

How a Kinase Inhibitor Withstands Gatekeeper Residue Mutations.

Mondal J, Tiwary P, Berne BJ.

J Am Chem Soc. 2016 Apr 6;138(13):4608-15. doi: 10.1021/jacs.6b01232. Epub 2016 Mar 22.

PMID:
26954686
11.

Spectral gap optimization of order parameters for sampling complex molecular systems.

Tiwary P, Berne BJ.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):2839-44. doi: 10.1073/pnas.1600917113. Epub 2016 Feb 29.

12.

Role of water and steric constraints in the kinetics of cavity-ligand unbinding.

Tiwary P, Mondal J, Morrone JA, Berne BJ.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):12015-9. doi: 10.1073/pnas.1516652112. Epub 2015 Sep 14.

13.

How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory.

Mondal J, Halverson D, Li IT, Stirnemann G, Walker GC, Berne BJ.

Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):9270-5. doi: 10.1073/pnas.1511780112. Epub 2015 Jul 13.

14.

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.

Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R.

J Am Chem Soc. 2015 Feb 25;137(7):2695-703. doi: 10.1021/ja512751q. Epub 2015 Feb 12.

PMID:
25625324
15.

Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase.

Mondal J, Friesner RA, Berne BJ.

J Chem Theory Comput. 2014 Dec 9;10(12):5696-5705. Epub 2014 Nov 13.

16.

How force unfolding differs from chemical denaturation.

Stirnemann G, Kang SG, Zhou R, Berne BJ.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3413-8. doi: 10.1073/pnas.1400752111. Epub 2014 Feb 18.

17.

Interface-limited growth of heterogeneously nucleated ice in supercooled water.

Nistor RA, Markland TE, Berne BJ.

J Phys Chem B. 2014 Jan 23;118(3):752-60. doi: 10.1021/jp408832b. Epub 2014 Jan 14.

PMID:
24393086
18.

How hydrophobic drying forces impact the kinetics of molecular recognition.

Mondal J, Morrone JA, Berne BJ.

Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13277-82. doi: 10.1073/pnas.1312529110. Epub 2013 Jul 30.

19.

When does trimethylamine N-oxide fold a polymer chain and urea unfold it?

Mondal J, Stirnemann G, Berne BJ.

J Phys Chem B. 2013 Jul 25;117(29):8723-32. doi: 10.1021/jp405609j. Epub 2013 Jul 10.

20.

Elasticity, structure, and relaxation of extended proteins under force.

Stirnemann G, Giganti D, Fernandez JM, Berne BJ.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3847-52. doi: 10.1073/pnas.1300596110. Epub 2013 Feb 13.

21.

Are hydrodynamic interactions important in the kinetics of hydrophobic collapse?

Li J, Morrone JA, Berne BJ.

J Phys Chem B. 2012 Sep 20;116(37):11537-44. Epub 2012 Sep 10.

PMID:
22931395
22.

Rate limit of protein elastic response is tether dependent.

Berkovich R, Hermans RI, Popa I, Stirnemann G, Garcia-Manyes S, Berne BJ, Fernandez JM.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14416-21. doi: 10.1073/pnas.1212167109. Epub 2012 Aug 15.

23.

Unraveling quantum mechanical effects in water using isotopic fractionation.

Markland TE, Berne BJ.

Proc Natl Acad Sci U S A. 2012 May 22;109(21):7988-91. doi: 10.1073/pnas.1203365109. Epub 2012 May 7.

24.

Theory and simulations of quantum glass forming liquids.

Markland TE, Morrone JA, Miyazaki K, Berne BJ, Reichman DR, Rabani E.

J Chem Phys. 2012 Feb 21;136(7):074511. doi: 10.1063/1.3684881.

PMID:
22360252
25.

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities.

Wang L, Berne BJ, Friesner RA.

Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):1937-42. doi: 10.1073/pnas.1114017109. Epub 2012 Jan 23.

26.

Interplay between hydrodynamics and the free energy surface in the assembly of nanoscale hydrophobes.

Morrone JA, Li J, Berne BJ.

J Phys Chem B. 2012 Jan 12;116(1):378-89. doi: 10.1021/jp209568n. Epub 2011 Dec 22.

PMID:
22142269
27.

Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).

Wang L, Friesner RA, Berne BJ.

J Phys Chem B. 2011 Aug 4;115(30):9431-8. doi: 10.1021/jp204407d. Epub 2011 Jul 7. Erratum in: J Phys Chem B. 2011 Sep 29;115(38):11305.

28.

Comment on "urea-mediated protein denaturation: a consensus view".

Zhou R, Li J, Hua L, Yang Z, Berne BJ.

J Phys Chem B. 2011 Feb 10;115(5):1323-6; discussion 1327-8. doi: 10.1021/jp105160a. Epub 2011 Jan 19. No abstract available.

29.

Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances.

Morrone JA, Markland TE, Ceriotti M, Berne BJ.

J Chem Phys. 2011 Jan 7;134(1):014103. doi: 10.1063/1.3518369.

PMID:
21218993
30.

Ligand binding to protein-binding pockets with wet and dry regions.

Wang L, Berne BJ, Friesner RA.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1326-30. doi: 10.1073/pnas.1016793108. Epub 2011 Jan 4. Erratum in: Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):9220.

31.

A displaced-solvent functional analysis of model hydrophobic enclosures.

Abel R, Wang L, Friesner RA, Berne BJ.

J Chem Theory Comput. 2010 Aug 20;6(9):2924-2934.

32.
33.

Water's role in the force-induced unfolding of ubiquitin.

Li J, Fernandez JM, Berne BJ.

Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19284-9. doi: 10.1073/pnas.1013159107. Epub 2010 Oct 25.

34.

Thermal and structural stability of adsorbed proteins.

Sharma S, Berne BJ, Kumar SK.

Biophys J. 2010 Aug 9;99(4):1157-65. doi: 10.1016/j.bpj.2010.05.030.

35.
36.

Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

Kuo TL, Garcia-Manyes S, Li J, Barel I, Lu H, Berne BJ, Urbakh M, Klafter J, Fernández JM.

Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11336-40. doi: 10.1073/pnas.1006517107. Epub 2010 Jun 8.

37.

Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls.

Morrone JA, Zhou R, Berne BJ.

J Chem Theory Comput. 2010 Jun 8;6(6):1798-804. doi: 10.1021/ct100054k. Epub 2010 May 19.

PMID:
26615840
38.

Competition of electrostatic and hydrophobic interactions between small hydrophobes and model enclosures.

Wang L, Friesner RA, Berne BJ.

J Phys Chem B. 2010 Jun 3;114(21):7294-301. doi: 10.1021/jp100772w.

39.

Dewetting transitions in protein cavities.

Young T, Hua L, Huang X, Abel R, Friesner R, Berne BJ.

Proteins. 2010 Jun;78(8):1856-69. doi: 10.1002/prot.22699.

40.
41.

Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy.

Perez-Jimenez R, Li J, Kosuri P, Sanchez-Romero I, Wiita AP, Rodriguez-Larrea D, Chueca A, Holmgren A, Miranda-Vizuete A, Becker K, Cho SH, Beckwith J, Gelhaye E, Jacquot JP, Gaucher EA, Sanchez-Ruiz JM, Berne BJ, Fernandez JM.

Nat Struct Mol Biol. 2009 Aug;16(8):890-6. doi: 10.1038/nsmb.1627. Epub 2009 Jul 13. Erratum in: Nat Struct Mol Biol. 2009 Dec;16(12):1331. Gaucher, Eric [corrected to Gaucher, Eric A].

42.

Single homopolypeptide chains collapse into mechanically rigid conformations.

Dougan L, Li J, Badilla CL, Berne BJ, Fernandez JM.

Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12605-10. doi: 10.1073/pnas.0900678106. Epub 2009 Jun 19.

43.

Urea's action on hydrophobic interactions.

Zangi R, Zhou R, Berne BJ.

J Am Chem Soc. 2009 Feb 4;131(4):1535-41. doi: 10.1021/ja807887g.

PMID:
19123816
44.

Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding.

Hua L, Zhou R, Thirumalai D, Berne BJ.

Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):16928-33. doi: 10.1073/pnas.0808427105. Epub 2008 Oct 28.

45.

Dewetting and hydrophobic interaction in physical and biological systems.

Berne BJ, Weeks JD, Zhou R.

Annu Rev Phys Chem. 2009;60:85-103. doi: 10.1146/annurev.physchem.58.032806.104445. Review.

46.

A Systematic Comparison of Pairwise and Many-Body Silica Potentials.

Paramore S, Cheng L, Berne BJ.

J Chem Theory Comput. 2008 Oct 14;4(10):1698-708. doi: 10.1021/ct800244q.

PMID:
26620176
47.

Scanning tunneling microscopy images of alkane derivatives on graphite: role of electronic effects.

Ilan B, Florio GM, Hybertsen MS, Berne BJ, Flynn GW.

Nano Lett. 2008 Oct;8(10):3160-5. doi: 10.1021/nl8014186. Epub 2008 Sep 18.

PMID:
18798685
48.

Dissecting entropic coiling and poor solvent effects in protein collapse.

Gräter F, Heider P, Zangi R, Berne BJ.

J Am Chem Soc. 2008 Sep 3;130(35):11578-9. doi: 10.1021/ja802341q. Epub 2008 Aug 12.

PMID:
18693720
49.

Role of water in mediating the assembly of Alzheimer amyloid-beta Abeta16-22 protofilaments.

Krone MG, Hua L, Soto P, Zhou R, Berne BJ, Shea JE.

J Am Chem Soc. 2008 Aug 20;130(33):11066-72. doi: 10.1021/ja8017303. Epub 2008 Jul 29.

50.

Temperature dependence of dimerization and dewetting of large-scale hydrophobes: a molecular dynamics study.

Zangi R, Berne BJ.

J Phys Chem B. 2008 Jul 24;112(29):8634-44. doi: 10.1021/jp802135c. Epub 2008 Jun 26. Erratum in: J Phys Chem B. 2010 Jul 15;114(27):9084.

PMID:
18582012

Supplemental Content

Loading ...
Support Center