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Results: 1 to 20 of 31

1.

Molecular dynamics simulations and drug discovery.

Durrant JD, McCammon JA.

BMC Biol. 2011 Oct 28;9:71. doi: 10.1186/1741-7007-9-71. Review.

PMID:
22035460
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis.

Durrant JD, McCammon JA.

J Mol Graph Model. 2011 Nov;31:5-9. doi: 10.1016/j.jmgm.2011.07.008. Epub 2011 Aug 7.

PMID:
21880522
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies.

Lawrenz M, Baron R, Wang Y, McCammon JA.

J Chem Theory Comput. 2011 Jun 2;7(7):2224-2232.

PMID:
21811708
[PubMed]
Free PMC Article
4.

Alchemical free energy methods for drug discovery: progress and challenges.

Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS.

Curr Opin Struct Biol. 2011 Apr;21(2):150-60. doi: 10.1016/j.sbi.2011.01.011. Epub 2011 Feb 23. Review.

PMID:
21349700
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1.

Durrant JD, Hall L, Swift RV, Landon M, Schnaufer A, Amaro RE.

PLoS Negl Trop Dis. 2010 Aug 24;4(8):e803. doi: 10.1371/journal.pntd.0000803.

PMID:
20808768
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Structural and functional basis of resistance to neuraminidase inhibitors of influenza B viruses.

Oakley AJ, Barrett S, Peat TS, Newman J, Streltsov VA, Waddington L, Saito T, Tashiro M, McKimm-Breschkin JL.

J Med Chem. 2010 Sep 9;53(17):6421-31. doi: 10.1021/jm100621s.

PMID:
20695427
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Treatment of severe cases of pandemic (H1N1) 2009 influenza: review of antivirals and adjuvant therapy.

Bearman GM, Shankaran S, Elam K.

Recent Pat Antiinfect Drug Discov. 2010 Jun;5(2):152-6. Review.

PMID:
20334616
[PubMed - indexed for MEDLINE]
8.

Discovery and evaluation of 7-alkyl-1,5-bis-aryl-pyrazolopyridinones as highly potent, selective, and orally efficacious inhibitors of p38alpha mitogen-activated protein kinase.

Pettus LH, Wurz RP, Xu S, Herberich B, Henkle B, Liu Q, McBride HJ, Mu S, Plant MH, Saris CJ, Sherman L, Wong LM, Chmait S, Lee MR, Mohr C, Hsieh F, Tasker AS.

J Med Chem. 2010 Apr 8;53(7):2973-85. doi: 10.1021/jm100095x.

PMID:
20218619
[PubMed - indexed for MEDLINE]
9.

Towards accurate free energy calculations in ligand protein-binding studies.

Steinbrecher T, Labahn A.

Curr Med Chem. 2010;17(8):767-85. Review.

PMID:
20088755
[PubMed - indexed for MEDLINE]
10.

Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate).

Antonyuk SV, Strange RW, Ellis MJ, Bessho Y, Kuramitsu S, Inoue Y, Yokoyama S, Hasnain SS.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Dec 1;65(Pt 12):1209-13. doi: 10.1107/S1744309109044935. Epub 2009 Nov 27.

PMID:
20054113
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Alchemical free energy simulations for biological complexes: powerful but temperamental....

Aleksandrov A, Thompson D, Simonson T.

J Mol Recognit. 2010 Mar-Apr;23(2):117-27. doi: 10.1002/jmr.980. Review.

PMID:
19693787
[PubMed - indexed for MEDLINE]
12.

AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

Trott O, Olson AJ.

J Comput Chem. 2010 Jan 30;31(2):455-61. doi: 10.1002/jcc.21334.

PMID:
19499576
[PubMed - indexed for MEDLINE]
Free PMC Article
13.
14.

Computational fragment-based approach at PDB scale by protein local similarity.

Moriaud F, Doppelt-Azeroual O, Martin L, Oguievetskaia K, Koch K, Vorotyntsev A, Adcock SA, Delfaud F.

J Chem Inf Model. 2009 Feb;49(2):280-94. doi: 10.1021/ci8003094.

PMID:
19434830
[PubMed - indexed for MEDLINE]
15.

Efficient synthesis of highly active phospha-isosteres of the influenza neuraminidase inhibitor oseltamivir.

Carbain B, Collins PJ, Callum L, Martin SR, Hay AJ, McCauley J, Streicher H.

ChemMedChem. 2009 Mar;4(3):335-7. doi: 10.1002/cmdc.200800379.

PMID:
19156651
[PubMed - indexed for MEDLINE]
16.

Computations of standard binding free energies with molecular dynamics simulations.

Deng Y, Roux B.

J Phys Chem B. 2009 Feb 26;113(8):2234-46. doi: 10.1021/jp807701h. Review.

PMID:
19146384
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Crystal structure of the NanB sialidase from Streptococcus pneumoniae.

Xu G, Potter JA, Russell RJ, Oggioni MR, Andrew PW, Taylor GL.

J Mol Biol. 2008 Dec 12;384(2):436-49. doi: 10.1016/j.jmb.2008.09.032. Epub 2008 Sep 21.

PMID:
18835278
[PubMed - indexed for MEDLINE]
18.
19.

Structural characterization of the 1918 influenza virus H1N1 neuraminidase.

Xu X, Zhu X, Dwek RA, Stevens J, Wilson IA.

J Virol. 2008 Nov;82(21):10493-501. doi: 10.1128/JVI.00959-08. Epub 2008 Aug 20.

PMID:
18715929
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil CR.

Br J Pharmacol. 2008 Mar;153 Suppl 1:S7-26. Epub 2007 Nov 26. Review.

PMID:
18037925
[PubMed - indexed for MEDLINE]
Free PMC Article

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