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Items: 1 to 20 of 99

1.

Identification of simple reaction coordinates from complex dynamics.

McGibbon RT, Husic BE, Pande VS.

J Chem Phys. 2017 Jan 28;146(4):044109. doi: 10.1063/1.4974306.

2.

Principal component analysis of molecular dynamics: on the use of Cartesian vs. internal coordinates.

Sittel F, Jain A, Stock G.

J Chem Phys. 2014 Jul 7;141(1):014111. doi: 10.1063/1.4885338.

PMID:
25005281
3.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
4.

The discovery of compounds that stimulate the activity of kallikrein-related peptidase 3 (KLK3).

Härkönen HH, Mattsson JM, Määttä JA, Stenman UH, Koistinen H, Matero S, Windshügel B, Poso A, Lahtela-Kakkonen M.

ChemMedChem. 2011 Dec 9;6(12):2170-8. doi: 10.1002/cmdc.201100349. Epub 2011 Sep 27. Erratum in: ChemMedChem. 2011 Dec 9;6(12):2123.

PMID:
21953896
5.

Kinetic distance and kinetic maps from molecular dynamics simulation.

Noé F, Clementi C.

J Chem Theory Comput. 2015 Oct 13;11(10):5002-11. doi: 10.1021/acs.jctc.5b00553. Epub 2015 Sep 11.

PMID:
26574285
6.

Flat SAR of P3-methylsulphonamide based small molecule legumain inhibitors.

Ness KA, Eddie SL, Burton S, Harrison T, Mullan P, Williams R.

Bioorg Med Chem Lett. 2016 Jan 15;26(2):413-416. doi: 10.1016/j.bmcl.2015.11.101. Epub 2015 Nov 28.

PMID:
26653614
7.

Modeling of babesipain-1 and identification of natural and synthetic leads for bovine babesiosis drug development.

Meetei PA, Rathore RS, Prabhu NP, Vindal V.

J Mol Model. 2016 Apr;22(4):71. doi: 10.1007/s00894-016-2945-9. Epub 2016 Mar 11.

PMID:
26969677
8.

Solid-phase synthesis of a library based on biphenyl-containing trypsin-like serine protease inhibitors.

Shi S, Zhu S, Gerritz SW, Rachwal B, Ruan Z, Hutchins R, Kakarla R, Sofia MJ, Sutton J, Cheney D.

Bioorg Med Chem Lett. 2009 Nov 15;19(22):6477-80. doi: 10.1016/j.bmcl.2009.08.100. Epub 2009 Sep 17.

PMID:
19804972
9.

Exploration of the structural requirements of HIV-protease inhibitors using pharmacophore, virtual screening and molecular docking approaches for lead identification.

Islam MA, Pillay TS.

J Mol Graph Model. 2015 Mar;56:20-30. doi: 10.1016/j.jmgm.2014.11.015. Epub 2014 Dec 5.

PMID:
25541527
10.

Current Progress in the Development of Metalloprotein Inhibitors.

Liao C.

Curr Top Med Chem. 2016;16(4):383. No abstract available.

PMID:
26281912
11.

Discovery of novel small molecule inhibitors of dengue viral NS2B-NS3 protease using virtual screening and scaffold hopping.

Deng J, Li N, Liu H, Zuo Z, Liew OW, Xu W, Chen G, Tong X, Tang W, Zhu J, Zuo J, Jiang H, Yang CG, Li J, Zhu W.

J Med Chem. 2012 Jul 26;55(14):6278-93. doi: 10.1021/jm300146f. Epub 2012 Jul 11.

PMID:
22742496
12.

Design and synthesis of a series of serine derivatives as small molecule inhibitors of the SARS coronavirus 3CL protease.

Konno H, Wakabayashi M, Takanuma D, Saito Y, Akaji K.

Bioorg Med Chem. 2016 Mar 15;24(6):1241-54. doi: 10.1016/j.bmc.2016.01.052. Epub 2016 Jan 29.

PMID:
26879854
13.

A benchmark for reaction coordinates in the transition path ensemble.

Li W, Ma A.

J Chem Phys. 2016 Apr 7;144(13):134104. doi: 10.1063/1.4945337.

14.

Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach.

Raman EP, Yu W, Lakkaraju SK, MacKerell AD Jr.

J Chem Inf Model. 2013 Dec 23;53(12):3384-98. doi: 10.1021/ci4005628. Epub 2013 Nov 25.

15.

Internal coordinate molecular dynamics: a foundation for multiscale dynamics.

Vaidehi N, Jain A.

J Phys Chem B. 2015 Jan 29;119(4):1233-42. doi: 10.1021/jp509136y. Epub 2015 Jan 6.

16.

Force-field modeling through quantum mechanical calculations: molecular dynamics simulations of a nematogenic molecule in its condensed phases.

Cacelli I, Lami CF, Prampolini G.

J Comput Chem. 2009 Feb;30(3):366-78. doi: 10.1002/jcc.21062.

PMID:
18629805
17.

Small-molecule probe using dual signals to monitor leucine aminopeptidase activity.

Yoon HY, Shim SH, Baek LJ, Hong JI.

Bioorg Med Chem Lett. 2011 Apr 15;21(8):2403-5. doi: 10.1016/j.bmcl.2011.02.068. Epub 2011 Feb 18.

PMID:
21396812
18.

Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics.

Xue Y, Skrynnikov NR.

Protein Sci. 2014 Apr;23(4):488-507. doi: 10.1002/pro.2433.

19.

Novel peptidyl aryl vinyl sulfones as highly potent and selective inhibitors of cathepsins L and B.

Mendieta L, Picó A, Tarragó T, Teixidó M, Castillo M, Rafecas L, Moyano A, Giralt E.

ChemMedChem. 2010 Sep 3;5(9):1556-67. doi: 10.1002/cmdc.201000109.

PMID:
20652927
20.

Inhibition of a viral enzyme by a small-molecule dimer disruptor.

Shahian T, Lee GM, Lazic A, Arnold LA, Velusamy P, Roels CM, Guy RK, Craik CS.

Nat Chem Biol. 2009 Sep;5(9):640-6. doi: 10.1038/nchembio.192. Epub 2009 Jul 26.

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