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Items: 1 to 20 of 543

1.

Hybrid finite element and Brownian dynamics method for charged particles.

Huber GA, Miao Y, Zhou S, Li B, McCammon JA.

J Chem Phys. 2016 Apr 28;144(16):164107. doi: 10.1063/1.4947086.

PMID:
27131531
2.

Molecular dynamic study of MlaC protein in Gram-negative bacteria: conformational flexibility, solvent effect and protein-phospholipid binding.

Huang YM, Miao Y, Munguia J, Lin L, Nizet V, McCammon JA.

Protein Sci. 2016 Apr 25. doi: 10.1002/pro.2939. [Epub ahead of print]

PMID:
27111825
3.

Development of Potent and Selective Inhibitors for Group VIA Calcium-Independent Phospholipase A2 Guided by Molecular Dynamics and Structure-Activity Relationships.

Mouchlis VD, Limnios D, Kokotou MG, Barbayianni E, Kokotos G, McCammon JA, Dennis EA.

J Med Chem. 2016 Apr 28. [Epub ahead of print]

PMID:
27087127
4.

Accelerated Molecular Dynamics Simulations of Protein Folding.

Miao Y, Feixas F, Eun C, McCammon JA.

J Comput Chem. 2016 Mar 5;37(6). doi: 10.1002/jcc.24337. No abstract available.

PMID:
26860347
5.

General trends of dihedral conformational transitions in a globular protein.

Miao Y, Baudry J, Smith JC, McCammon JA.

Proteins. 2016 Apr;84(4):501-14. doi: 10.1002/prot.24996. Epub 2016 Feb 15.

PMID:
26799251
6.

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

Sun H, Wen J, Zhao Y, Li B, McCammon JA.

J Chem Phys. 2015 Dec 28;143(24):243110. doi: 10.1063/1.4932336.

PMID:
26723595
7.

Antiinfectives targeting enzymes and the proton motive force.

Feng X, Zhu W, Schurig-Briccio LA, Lindert S, Shoen C, Hitchings R, Li J, Wang Y, Baig N, Zhou T, Kim BK, Crick DC, Cynamon M, McCammon JA, Gennis RB, Oldfield E.

Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):E7073-82. doi: 10.1073/pnas.1521988112. Epub 2015 Dec 7.

PMID:
26644565
8.

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor.

Kappel K, Miao Y, McCammon JA.

Q Rev Biophys. 2015 Nov;48(4):479-87. doi: 10.1017/S0033583515000153.

PMID:
26537408
9.

Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.

Kim MO, Blachly PG, McCammon JA.

PLoS Comput Biol. 2015 Oct 27;11(10):e1004341. doi: 10.1371/journal.pcbi.1004341. eCollection 2015 Oct.

10.

Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation.

Cheng Y, Rao V, Tu AY, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M.

J Biol Chem. 2015 Nov 13;290(46):27749-66. doi: 10.1074/jbc.M115.683045. Epub 2015 Sep 21.

PMID:
26391394
11.

Electrostatic steering enhances the rate of cAMP binding to phosphodiesterase: Brownian dynamics modeling.

Huang YM, Huber G, McCammon JA.

Protein Sci. 2015 Nov;24(11):1884-9. doi: 10.1002/pro.2794. Epub 2015 Sep 8.

PMID:
26346301
12.

Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling.

Kekenes-Huskey PM, Eun C, McCammon JA.

J Chem Phys. 2015 Sep 7;143(9):094103. doi: 10.1063/1.4929528.

PMID:
26342355
13.

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.

Miao Y, Feher VA, McCammon JA.

J Chem Theory Comput. 2015 Aug 11;11(8):3584-3595. Epub 2015 Jul 14.

PMID:
26300708
14.

Computation of pH-dependent binding free energies.

Kim MO, McCammon JA.

Biopolymers. 2016 Jan;105(1):43-9. doi: 10.1002/bip.22702. Review.

PMID:
26202905
15.

Broken-Symmetry DFT Computations for the Reaction Pathway of IspH, an Iron-Sulfur Enzyme in Pathogenic Bacteria.

Blachly PG, Sandala GM, Giammona DA, Bashford D, McCammon JA, Noodleman L.

Inorg Chem. 2015 Jul 6;54(13):6439-61. doi: 10.1021/acs.inorgchem.5b00751. Epub 2015 Jun 22.

PMID:
26098647
16.

Accelerated molecular dynamics simulations of protein folding.

Miao Y, Feixas F, Eun C, McCammon JA.

J Comput Chem. 2015 Jul 30;36(20):1536-49. doi: 10.1002/jcc.23964. Epub 2015 Jun 12.

PMID:
26096263
17.

Substrate channeling between the human dihydrofolate reductase and thymidylate synthase.

Wang N, McCammon JA.

Protein Sci. 2016 Jan;25(1):79-86. doi: 10.1002/pro.2720. Epub 2015 Jun 29.

PMID:
26096018
18.

How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L.

J Chem Theory Comput. 2015 Jun 9;11(6):2670-9. doi: 10.1021/acs.jctc.5b00214.

PMID:
26085821
19.

Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach.

Guo Z, Li B, Cheng LT, Zhou S, McCammon JA, Che J.

J Chem Theory Comput. 2015 Feb 10;11(2):753-65. doi: 10.1021/ct500867u.

20.

Enhanced ligand sampling for relative protein-ligand binding free energy calculations.

Kaus JW, McCammon JA.

J Phys Chem B. 2015 May 21;119(20):6190-7. doi: 10.1021/acs.jpcb.5b02348. Epub 2015 May 8.

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