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Results: 1 to 20 of 500

1.

Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free Energies.

Kim MO, Blachly PG, Kaus JW, McCammon JA.

J Phys Chem B. 2014 Aug 25. [Epub ahead of print]

PMID:
25134690
[PubMed - as supplied by publisher]
2.

Trypsinogen activation as observed in accelerated molecular dynamics simulations.

Boechi L, Pierce L, Komives EA, McCammon JA.

Protein Sci. 2014 Aug 11. doi: 10.1002/pro.2532. [Epub ahead of print]

PMID:
25131668
[PubMed - as supplied by publisher]
3.

Exploring the Influence of the Protein Environment on Metal-Binding Pharmacophores.

Martin DP, Blachly PG, McCammon JA, Cohen SM.

J Med Chem. 2014 Aug 19. [Epub ahead of print]

PMID:
25116076
[PubMed - as supplied by publisher]
4.

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.

Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA.

J Chem Theory Comput. 2014 Jul 8;10(7):2677-2689. Epub 2014 May 1.

PMID:
25061441
[PubMed]
5.

Computer-Aided Drug Discovery Approach Finds Calcium Sensitizer of Cardiac Troponin.

Lindert S, Li MX, Sykes BD, McCammon JA.

Chem Biol Drug Des. 2014 Jun 20. doi: 10.1111/cbdd.12381. [Epub ahead of print]

PMID:
24954187
[PubMed - as supplied by publisher]
6.

Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site.

Liu YL, Lindert S, Zhu W, Wang K, McCammon JA, Oldfield E.

Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):E2530-9. doi: 10.1073/pnas.1409061111. Epub 2014 Jun 9.

PMID:
24927548
[PubMed - indexed for MEDLINE]
7.

Molecular dynamics simulation study of conformational changes of transcription factor TFIIS during RNA polymerase II transcriptional arrest and reactivation.

Eun C, Ortiz-Sánchez JM, Da L, Wang D, McCammon JA.

PLoS One. 2014 May 19;9(5):e97975. doi: 10.1371/journal.pone.0097975. eCollection 2014.

PMID:
24842057
[PubMed - in process]
Free PMC Article
8.

Undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads.

Sinko W, Wang Y, Zhu W, Zhang Y, Feixas F, Cox CL, Mitchell DA, Oldfield E, McCammon JA.

J Med Chem. 2014 Jul 10;57(13):5693-701. doi: 10.1021/jm5004649. Epub 2014 Jun 24.

PMID:
24827744
[PubMed - in process]
9.

Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation.

Kekenes-Huskey PM, Gillette AK, McCammon JA.

J Chem Phys. 2014 May 7;140(17):174106. doi: 10.1063/1.4873382.

PMID:
24811624
[PubMed - in process]
10.

Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields.

Götz AW, Bucher D, Lindert S, McCammon JA.

J Chem Theory Comput. 2014 Apr 8;10(4):1631-1637. Epub 2014 Mar 4.

PMID:
24803868
[PubMed]
11.

Variational Implicit Solvation with Poisson-Boltzmann Theory.

Zhou S, Cheng LT, Dzubiella J, Li B, McCammon JA.

J Chem Theory Comput. 2014 Apr 8;10(4):1454-1467. Epub 2014 Feb 21.

PMID:
24803864
[PubMed]
12.

Heterogeneous Hydration of p53/MDM2 Complex.

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

J Chem Theory Comput. 2014 Mar 11;10(3):1302-1313. Epub 2014 Jan 31.

PMID:
24803860
[PubMed]
13.

Accelerated adaptive integration method.

Kaus JW, Arrar M, McCammon JA.

J Phys Chem B. 2014 May 15;118(19):5109-18. doi: 10.1021/jp502358y. Epub 2014 May 6.

PMID:
24780083
[PubMed - in process]
14.

'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site.

Martin DP, Blachly PG, Marts AR, Woodruff TM, de Oliveira CA, McCammon JA, Tierney DL, Cohen SM.

J Am Chem Soc. 2014 Apr 9;136(14):5400-6. doi: 10.1021/ja500616m. Epub 2014 Mar 27.

PMID:
24635441
[PubMed - in process]
15.

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

Lindert S, Bucher D, Eastman P, Pande V, McCammon JA.

J Chem Theory Comput. 2013 Nov 12;9(11):4684-4691. Epub 2013 Oct 15.

PMID:
24634618
[PubMed]
Free PMC Article
16.

A model study of sequential enzyme reactions and electrostatic channeling.

Eun C, Kekenes-Huskey PM, Metzger VT, McCammon JA.

J Chem Phys. 2014 Mar 14;140(10):105101. doi: 10.1063/1.4867286.

PMID:
24628210
[PubMed - in process]
17.

Drug screening strategy for human membrane proteins: from NMR protein backbone structure to in silica- and NMR-screened hits.

Lindert S, Maslennikov I, Chiu EJ, Pierce LC, McCammon JA, Choe S.

Biochem Biophys Res Commun. 2014 Mar 21;445(4):724-33. doi: 10.1016/j.bbrc.2014.01.179. Epub 2014 Feb 10.

PMID:
24525125
[PubMed - indexed for MEDLINE]
18.

Structural and computational studies of the Staphylococcus aureus sortase B-substrate complex reveal a substrate-stabilized oxyanion hole.

Jacobitz AW, Wereszczynski J, Yi SW, Amer BR, Huang GL, Nguyen AV, Sawaya MR, Jung ME, McCammon JA, Clubb RT.

J Biol Chem. 2014 Mar 28;289(13):8891-902. doi: 10.1074/jbc.M113.509273. Epub 2014 Feb 11.

PMID:
24519933
[PubMed - indexed for MEDLINE]
19.

Identification and validation of modulators of exchange protein activated by cAMP (Epac) activity: structure-function implications for Epac activation and inhibition.

Brown LM, Rogers KE, McCammon JA, Insel PA.

J Biol Chem. 2014 Mar 21;289(12):8217-30. doi: 10.1074/jbc.M114.548636. Epub 2014 Feb 4.

PMID:
24497631
[PubMed - indexed for MEDLINE]
20.

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics.

Miao Y, Nichols SE, McCammon JA.

Phys Chem Chem Phys. 2014 Apr 14;16(14):6398-406. doi: 10.1039/c3cp53962h. Epub 2014 Jan 21.

PMID:
24445284
[PubMed - in process]
Free PMC Article

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