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Items: 19

1.

Binding Specificity Determines the Cytochrome P450 3A4 Mediated Enantioselective Metabolism of Metconazole.

Zhuang S, Zhang L, Zhan T, Lu L, Zhao L, Wang H, Morrone JA, Liu W, Zhou R.

J Phys Chem B. 2018 Jan 25;122(3):1176-1184. doi: 10.1021/acs.jpcb.7b11170. Epub 2018 Jan 12.

PMID:
29310431
2.

Accelerating physical simulations of proteins by leveraging external knowledge.

Perez A, Morrone JA, Dill KA.

Wiley Interdiscip Rev Comput Mol Sci. 2017 Sep-Oct;7(5). pii: e1309. doi: 10.1002/wcms.1309. Epub 2017 Apr 19.

3.

Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics.

Morrone JA, Perez A, MacCallum J, Dill KA.

J Chem Theory Comput. 2017 Feb 14;13(2):870-876. doi: 10.1021/acs.jctc.6b00977. Epub 2017 Jan 19.

PMID:
28042966
4.

Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX.

Morrone JA, Perez A, Deng Q, Ha SN, Holloway MK, Sawyer TK, Sherborne BS, Brown FK, Dill KA.

J Chem Theory Comput. 2017 Feb 14;13(2):863-869. doi: 10.1021/acs.jctc.6b00978. Epub 2017 Jan 19.

PMID:
28042965
5.

Blind protein structure prediction using accelerated free-energy simulations.

Perez A, Morrone JA, Brini E, MacCallum JL, Dill KA.

Sci Adv. 2016 Nov 11;2(11):e1601274. eCollection 2016 Nov.

6.

Advances in free-energy-based simulations of protein folding and ligand binding.

Perez A, Morrone JA, Simmerling C, Dill KA.

Curr Opin Struct Biol. 2016 Feb;36:25-31. doi: 10.1016/j.sbi.2015.12.002. Epub 2016 Jan 7. Review.

7.

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.

8.

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.

9.

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
10.

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
11.

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
12.

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
13.

Displaced path integral formulation for the momentum distribution of quantum particles.

Lin L, Morrone JA, Car R, Parrinello M.

Phys Rev Lett. 2010 Sep 10;105(11):110602. Epub 2010 Sep 9.

PMID:
20867559
14.

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
15.

Tunneling and delocalization effects in hydrogen bonded systems: a study in position and momentum space.

Morrone JA, Lin L, Car R.

J Chem Phys. 2009 May 28;130(20):204511. doi: 10.1063/1.3142828.

PMID:
19485461
16.

Nuclear quantum effects in water.

Morrone JA, Car R.

Phys Rev Lett. 2008 Jul 4;101(1):017801. Epub 2008 Jul 1.

PMID:
18764152
17.

Proton momentum distribution in water: an open path integral molecular dynamics study.

Morrone JA, Srinivasan V, Sebastiani D, Car R.

J Chem Phys. 2007 Jun 21;126(23):234504.

PMID:
17600422
18.

Ab initio molecular dynamics simulation of the structure and proton transport dynamics of methanol-water solutions.

Morrone JA, Haslinger KE, Tuckerman ME.

J Phys Chem B. 2006 Mar 2;110(8):3712-20.

PMID:
16494428
19.

Long range interactions on wires: a reciprocal space based formalism.

Mináry P, Morrone JA, Yarne DA, Tuckerman ME, Martyna GJ.

J Chem Phys. 2004 Dec 15;121(23):11949-56.

PMID:
15634157

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