Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 56

1.

Performance of a docking/molecular dynamics protocol for virtual screening of nutlin-class inhibitors of Mdmx.

Bharatham N, Finch KE, Min J, Mayasundari A, Dyer MA, Guy RK, Bashford D.

J Mol Graph Model. 2017 Jun;74:54-60. doi: 10.1016/j.jmgm.2017.02.014. Epub 2017 Feb 24.

2.

Monitoring Ligand-Induced Protein Ordering in Drug Discovery.

Grace CR, Ban D, Min J, Mayasundari A, Min L, Finch KE, Griffiths L, Bharatham N, Bashford D, Kiplin Guy R, Dyer MA, Kriwacki RW.

J Mol Biol. 2016 Mar 27;428(6):1290-1303. doi: 10.1016/j.jmb.2016.01.016. Epub 2016 Jan 23.

3.

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.

4.

Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition.

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

J Chem Theory Comput. 2014 Sep 9;10(9):3871-3884. Epub 2014 Aug 13.

5.

HLA-DRB1*07:01 is associated with a higher risk of asparaginase allergies.

Fernandez CA, Smith C, Yang W, Daté M, Bashford D, Larsen E, Bowman WP, Liu C, Ramsey LB, Chang T, Turner V, Loh ML, Raetz EA, Winick NJ, Hunger SP, Carroll WL, Onengut-Gumuscu S, Chen WM, Concannon P, Rich SS, Scheet P, Jeha S, Pui CH, Evans WE, Devidas M, Relling MV.

Blood. 2014 Aug 21;124(8):1266-76. doi: 10.1182/blood-2014-03-563742. Epub 2014 Jun 26.

6.

Identification and characterization of an allosteric inhibitory site on dihydropteroate synthase.

Hammoudeh DI, Daté M, Yun MK, Zhang W, Boyd VA, Viacava Follis A, Griffith E, Lee RE, Bashford D, White SW.

ACS Chem Biol. 2014 Jun 20;9(6):1294-302. doi: 10.1021/cb500038g. Epub 2014 Mar 27.

7.

Ligand binding mode prediction by docking: mdm2/mdmx inhibitors as a case study.

Bharatham N, Bharatham K, Shelat AA, Bashford D.

J Chem Inf Model. 2014 Feb 24;54(2):648-59. doi: 10.1021/ci4004656. Epub 2014 Jan 21.

8.

Catalysis and sulfa drug resistance in dihydropteroate synthase.

Yun MK, Wu Y, Li Z, Zhao Y, Waddell MB, Ferreira AM, Lee RE, Bashford D, White SW.

Science. 2012 Mar 2;335(6072):1110-4. doi: 10.1126/science.1214641.

9.

Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily.

Gajewski S, Comeaux EQ, Jafari N, Bharatham N, Bashford D, White SW, van Waardenburg RC.

J Mol Biol. 2012 Jan 27;415(4):741-58. doi: 10.1016/j.jmb.2011.11.044. Epub 2011 Dec 6. Erratum in: J Mol Biol. 2012 Mar 9;416(5):725.

10.
11.

Incomplete folding upon binding mediates Cdk4/cyclin D complex activation by tyrosine phosphorylation of inhibitor p27 protein.

Ou L, Ferreira AM, Otieno S, Xiao L, Bashford D, Kriwacki RW.

J Biol Chem. 2011 Aug 26;286(34):30142-51. doi: 10.1074/jbc.M111.244095. Epub 2011 Jun 29.

12.
13.

Identification and characterization of the first small molecule inhibitor of MDMX.

Reed D, Shen Y, Shelat AA, Arnold LA, Ferreira AM, Zhu F, Mills N, Smithson DC, Regni CA, Bashford D, Cicero SA, Schulman BA, Jochemsen AG, Guy RK, Dyer MA.

J Biol Chem. 2010 Apr 2;285(14):10786-96. doi: 10.1074/jbc.M109.056747. Epub 2010 Jan 15.

14.

Quantitative structure-activity relationship (QSAR) for a series of novel cannabinoid derivatives using descriptors derived from semi-empirical quantum-chemical calculations.

Ferreira AM, Krishnamurthy M, Moore BM 2nd, Finkelstein D, Bashford D.

Bioorg Med Chem. 2009 Mar 15;17(6):2598-606. doi: 10.1016/j.bmc.2008.11.059. Epub 2008 Dec 3.

PMID:
19250829
15.

Rational design of the first small-molecule antagonists of NHERF1/EBP50 PDZ domains.

Mayasundari A, Ferreira AM, He L, Mahindroo N, Bashford D, Fujii N.

Bioorg Med Chem Lett. 2008 Feb 1;18(3):942-5. doi: 10.1016/j.bmcl.2007.12.038. Epub 2007 Dec 23.

PMID:
18180157
16.

Experimental and DFT studies: novel structural modifications greatly enhance the solvent sensitivity of live cell imaging dyes.

Toutchkine A, Han WG, Ullmann M, Liu T, Bashford D, Noodleman L, Hahn KM.

J Phys Chem A. 2007 Oct 25;111(42):10849-60. Epub 2007 Oct 5.

17.

A fluid salt-bridging cluster and the stabilization of p53.

Lwin TZ, Durant JJ, Bashford D.

J Mol Biol. 2007 Nov 9;373(5):1334-47. Epub 2007 Aug 24.

18.
19.

Disordered p27Kip1 exhibits intrinsic structure resembling the Cdk2/cyclin A-bound conformation.

Sivakolundu SG, Bashford D, Kriwacki RW.

J Mol Biol. 2005 Nov 11;353(5):1118-28. Epub 2005 Sep 20.

PMID:
16214166
20.

On the role of the conserved aspartate in the hydrolysis of the phosphocysteine intermediate of the low molecular weight tyrosine phosphatase.

Asthagiri D, Liu T, Noodleman L, Van Etten RL, Bashford D.

J Am Chem Soc. 2004 Oct 6;126(39):12677-84.

PMID:
15453802
21.
22.

Macroscopic electrostatic models for protonation states in proteins.

Bashford D.

Front Biosci. 2004 May 1;9:1082-99. Review.

PMID:
14977531
23.

A theoretical study of the UV/visible absorption and emission solvatochromic properties of solvent-sensitive dyes.

Han WG, Liu T, Himo F, Toutchkine A, Bashford D, Hahn KM, Noodleman L.

Chemphyschem. 2003 Oct 17;4(10):1084-94.

PMID:
14596006
24.

Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle.

Onufriev A, Smondyrev A, Bashford D.

J Mol Biol. 2003 Oct 3;332(5):1183-93.

PMID:
14499620
25.

Photoisomerization and proton transfer in photoactive yellow protein.

Thompson MJ, Bashford D, Noodleman L, Getzoff ED.

J Am Chem Soc. 2003 Jul 9;125(27):8186-94.

PMID:
12837088
26.

Structural details, pathways, and energetics of unfolding apomyoglobin.

Onufriev A, Case DA, Bashford D.

J Mol Biol. 2003 Jan 17;325(3):555-67.

PMID:
12498802
27.

Effective Born radii in the generalized Born approximation: the importance of being perfect.

Onufriev A, Case DA, Bashford D.

J Comput Chem. 2002 Nov 15;23(14):1297-304.

PMID:
12214312
28.

Density functional study of the mechanism of a tyrosine phosphatase: I. Intermediate formation.

Asthagiri D, Dillet V, Liu T, Noodleman L, Van Etten RL, Bashford D.

J Am Chem Soc. 2002 Aug 28;124(34):10225-35.

PMID:
12188687
29.

Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair.

Beuning PJ, Nagan MC, Cramer CJ, Musier-Forsyth K, Gelpí JL, Bashford D.

RNA. 2002 May;8(5):659-70.

30.

Continuum and atomistic modeling of ion partitioning into a peptide nanotube.

Asthagiri D, Bashford D.

Biophys J. 2002 Mar;82(3):1176-89.

31.

CuZn Superoxide Dismutase Geometry Optimization, Energetics, and Redox Potential Calculations by Density Functional and Electrostatic Methods.

Konecny R, Li J, Fisher CL, Dillet V, Bashford D, Noodleman L.

Inorg Chem. 1999 Mar 8;38(5):940-950.

PMID:
11670866
32.

Density Functional and Electrostatic Calculations of Manganese Superoxide Dismutase Active Site Complexes in Protein Environments.

Li J, Fisher CL, Konecny R, Bashford D, Noodleman L.

Inorg Chem. 1999 Mar 8;38(5):929-939.

PMID:
11670865
33.

pK(a) Calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin.

Spassov VZ, Luecke H, Gerwert K, Bashford D.

J Mol Biol. 2001 Sep 7;312(1):203-19.

PMID:
11545597
34.
35.

Generalized born models of macromolecular solvation effects.

Bashford D, Case DA.

Annu Rev Phys Chem. 2000;51:129-52. Review.

PMID:
11031278
36.

Protonation states and pH titration in the photocycle of photoactive yellow protein.

Demchuk E, Genick UK, Woo TT, Getzoff ED, Bashford D.

Biochemistry. 2000 Feb 8;39(5):1100-13.

PMID:
10653656
37.
38.

Calculations of electrostatic interactions and pKas in the active site of Escherichia coli thioredoxin.

Dillet V, Dyson HJ, Bashford D.

Biochemistry. 1998 Jul 14;37(28):10298-306.

PMID:
9665738
39.

All-atom empirical potential for molecular modeling and dynamics studies of proteins.

MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M.

J Phys Chem B. 1998 Apr 30;102(18):3586-616. doi: 10.1021/jp973084f.

PMID:
24889800
41.

Thermodynamics of a reverse turn motif. Solvent effects and side-chain packing.

Demchuk E, Bashford D, Gippert GP, Case DA.

J Mol Biol. 1997 Jul 11;270(2):305-17.

PMID:
9236131
42.

Dynamics of a type VI reverse turn in a linear peptide in aqueous solution.

Demchuk E, Bashford D, Case DA.

Fold Des. 1997;2(1):35-46.

44.

Computational studies of the early intermediates of the bacteriorhodopsin photocycle.

Engels M, Gerwert K, Bashford D.

Biophys Chem. 1995 Sep-Oct;56(1-2):95-104.

PMID:
7662874
45.

Electrostatic calculations of side-chain pK(a) values in myoglobin and comparison with NMR data for histidines.

Bashford D, Case DA, Dalvit C, Tennant L, Wright PE.

Biochemistry. 1993 Aug 10;32(31):8045-56.

PMID:
8347606
46.

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin.

Bashford D, Gerwert K.

J Mol Biol. 1992 Mar 20;224(2):473-86.

PMID:
1313886
47.

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.

Bashford D, Karplus M.

Biochemistry. 1990 Nov 6;29(44):10219-25.

PMID:
2271649
48.

Electrostatic effects of charge perturbations introduced by metal oxidation in proteins. A theoretical analysis.

Bashford D, Karplus M, Canters GW.

J Mol Biol. 1988 Sep 20;203(2):507-10.

PMID:
3199443
49.

Diffusion-collision model for the folding kinetics of myoglobin.

Bashford D, Cohen FE, Karplus M, Kuntz ID, Weaver DL.

Proteins. 1988;4(3):211-27.

PMID:
3237719
50.

Determinants of a protein fold. Unique features of the globin amino acid sequences.

Bashford D, Chothia C, Lesk AM.

J Mol Biol. 1987 Jul 5;196(1):199-216.

PMID:
3656444

Supplemental Content

Loading ...
Support Center