Bashford, Donald: search on Z-Library

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1

A Theoretical Study of the UV/Visible Absorption and Emission Solvatochromic Properties of Solvent-Sensitive Dyes

Wen-Ge Han, Tiqing Liu, Fahmi Himo, Alexei Toutchkine, Donald Bashford, Klaus M. Hahn, Louis Noodleman

Journal:

Year:

2003

Language:

english

File:

PDF, 311 KB

english, 2003

2

Macroscopic electrostatic models for protonation states in proteins

Bashford, Donald

Journal:

Frontiers in Bioscience

Year:

2004

Language:

english

File:

PDF, 444 KB

english, 2004

3

Diffusion-Collision Model for the Folding Kinetics of the λ-Repressor Operator-Binding Domain

Bashford, Donald, Weaver, David L., Karplus, Martin

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

1984

Language:

english

File:

PDF, 582 KB

english, 1984

4

Incorporating Solvation Effects into Density Functional Electronic Structure Calculations

Chen, Jun L., Noodleman, Louis, Case, David A., Bashford, Donald

Journal:

Journal of Physical Chemistry

Year:

1994

Language:

english

File:

PDF, 1.37 MB

english, 1994

5

Experimental and DFT Studies: Novel Structural Modifications Greatly Enhance the Solvent Sensitivity of Live Cell Imaging Dyes

Toutchkine, Alexei, Han, Wen-Ge, Ullmann, Matthias, Liu, Tiqing, Bashford, Donald, Noodleman, Louis, Hahn, Klaus M.

Journal:

Journal of Physical Chemistry A

Year:

2007

Language:

english

File:

PDF, 456 KB

english, 2007

6

Monitoring ligand-induced protein ordering in drug discovery

Grace, Christy R., Ban, David, Min, Jaeki, Mayasundari, Anand, Min, Lie, Finch, Kristin E., Griffiths, Lyra, Bharatham, Nagakumar, Bashford, Donald, Kiplin Guy, R., Dyer, Michael A., Kriwacki, Richard

Journal:

Journal of Molecular Biology

Year:

2016

Language:

english

File:

PDF, 834 KB

english, 2016

7

Electrostatic effects in biological molecules

Bashford, Donald

Journal:

Current Opinion in Structural Biology

Year:

1991

Language:

english

File:

PDF, 1.09 MB

english, 1991

8

Modification of the Generalized Born Model Suitable for Macromolecules

Onufriev, Alexey, Bashford, Donald, Case, David A.

Journal:

Journal of Physical Chemistry B

Year:

2000

Language:

english

File:

PDF, 185 KB

english, 2000

9

A Computational Study of the Role of Solvation Effects in Reverse Turn Formation in the Tetrapeptides APGD and APGN

Bashford, Donald, Case, David A., Choi, Chris, Gippert, Garry P.

Journal:

Journal of the American Chemical Society

Year:

1997

Language:

english

File:

PDF, 233 KB

english, 1997

10

An analytical algorithm for the rapid determination of the solvent accessibility of points in a three-dimensional lattice around a solute molecule

Tony You, Donald Bashford

Journal:

Journal of Computational Chemistry

Year:

1995

Language:

english

File:

PDF, 1.31 MB

english, 1995

11

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

Eugene Demchuk, Donald Bashford, David A. Case

Journal:

Folding and Design

Year:

1997

Language:

english

File:

PDF, 645 KB

english, 1997

12

Determinants of a protein fold

Bashford, Donald, Chothia, Cyrus, Lesk, Arthur M.

Journal:

Journal of Molecular Biology

Year:

1987

Language:

english

File:

PDF, 2.04 MB

english, 1987

13

Photoisomerization and Proton Transfer in Photoactive Yellow Protein

Thompson, Michael J., Bashford, Donald, Noodleman, Louis, Getzoff, Elizabeth D.

Journal:

Journal of the American Chemical Society

Year:

2003

Language:

english

File:

PDF, 247 KB

english, 2003

14

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

Li, Jian, Fisher, Cindy L., Konecny, Robert, Bashford, Donald, Noodleman, Louis

Journal:

Inorganic Chemistry

Year:

1999

Language:

english

File:

PDF, 195 KB

english, 1999

15

Density Functional Vertical Self-Consistent Reaction Field Theory for Solvatochromism Studies of Solvent-Sensitive Dyes

Liu, Tiqing, Han, Wen-Ge, Himo, Fahmi, Ullmann, G. Matthias, Bashford, Donald, Toutchkine, Alexei, Hahn, Klaus M., Noodleman, Louis

Journal:

Journal of Physical Chemistry A

Year:

2004

Language:

english

File:

PDF, 243 KB

english, 2004

16

Exploring protein native states and large-scale conformational changes with a modified generalized born model

Alexey Onufriev, Donald Bashford, David A. Case

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 246 KB

english, 2004

17

Brownian dynamics simulation of protein folding: A study of the diffusion-collision model

Sangyoub Lee, Martin Karplus, Donald Bashford, David Weaver

Journal:

Year:

1987

Language:

english

File:

PDF, 1.25 MB

english, 1987

18

Mössbauer properties of the diferric cluster and the differential iron(ii)-binding affinity of the iron sites in protein R2 of class Ia Escherichia coli ribonucleotide reductase: a DFT/electrostatics study

Han, Wen-Ge, Sandala, Gregory M., Giammona, Debra Ann, Bashford, Donald, Noodleman, Louis

Journal:

Dalton Transactions

Year:

2011

Language:

english

File:

PDF, 1.47 MB

english, 2011

19

Fluctuation and rotation in diffusion-influenced monomolecular reactions

Bashford, Donald

Journal:

The Journal of Chemical Physics

Year:

1986

Language:

english

File:

PDF, 1.09 MB

english, 1986

20

NIH Public Access

Yun, Mi-kyung, Wu, Yinan, Li, Zhenmei, Zhao, Ying, Waddell, M Brett, Antonio, M, Lee, Richard E, Bashford, Donald, White, Stephen W

Year:

2012

Language:

english

File:

PDF, 2.95 MB

english, 2012

21

Solvation energy density occlusion approximation for evaluation of desolvation penalties in biomolecular interactions

Nidhi Arora, Donald Bashford

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 289 KB

english, 2001

22

Stabilization of Charges and Protonation States in the Active Site of the Protein Tyrosine Phosphatases: A Computational Study †

Dillet, Valérie, Van Etten, Robert L., Bashford, Donald

Journal:

Journal of Physical Chemistry B

Year:

2000

Language:

english

File:

PDF, 212 KB

english, 2000

23

Calculations of Electrostatic Interactions and p K a s in the Active Site of Escherichia coli Thioredoxin †,‡

Dillet, Valérie, Dyson, H. Jane, Bashford, Donald

Journal:

Year:

1998

Language:

english

File:

PDF, 135 KB

english, 1998

24

Electrostatic coupling to pH-titrating sites as a source of cooperativity in protein-ligand binding

Velin Spassov, Donald Bashford

Journal:

Protein Science

Year:

1998

Language:

english

File:

PDF, 5.80 MB

english, 1998

25

Use of 1 H NMR Spectroscopy and Computer Simulations To Analyze Histidine p K a Changes in a Protein Tyrosine Phosphatase: Experimental and Theoretical Determination of Electrostatic Properties in a Small Protein †

Tishmack, Patrick A., Bashford, Donald, Harms, Etti, Van Etten, Robert L.

Journal:

Year:

1997

Language:

english

File:

PDF, 409 KB

english, 1997

26

Model for Proton Transport Coupled to Protein Conformational Change: Application to Proton Pumping in the Bacteriorhodopsin Photocycle

Ferreira, Antonio M., Bashford, Donald

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 329 KB

english, 2006

27

SPIE Proceedings [SPIE Biomedical Optics 2006 - San Jose, CA (Saturday 21 January 2006)] Optical Molecular Probes for Biomedical Applications - Phthalocyanine dye as an extremely photostable and highly fluorescent near-infrared labeling reagent

Peng, Xinzhan, Draney, Daniel R., Volcheck, William M., Bashford, Gregory R., Lamb, Donald T., Grone, Daniel L., Zhang, Yonghong, Johnson, Craig M., Achilefu, Samuel, Bornhop, Darryl J., Raghavachari,

Year:

2006

Language:

english

File:

PDF, 399 KB

english, 2006

28

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

Eugene Demchuk, Donald Bashford, Garry P. Gippert, David A. Case

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 443 KB

english, 1997

29

Structure and Dynamics of Self-Assembling Peptide Nanotubes and the Channel-Mediated Water Organization and Self-Diffusion. A Molecular Dynamics Study

Engels, Michael, Bashford, Donald, Ghadiri, M. Reza

Journal:

Journal of the American Chemical Society

Year:

1995

Language:

english

File:

PDF, 2.39 MB

english, 1995

30

Multiple-site ligand binding to flexible macromolecules: Separation of global and local conformational change and an iterative mobile clustering approach

Velin Z. Spassov, Donald Bashford

Journal:

Journal of Computational Chemistry

Year:

1999

Language:

english

File:

PDF, 318 KB

english, 1999

31

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

Alexey Onufriev, David A. Case, Donald Bashford

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 203 KB

english, 2002

32

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

Antonio M. Ferreira, Mathangi Krishnamurthy, Bob M. Moore II, David Finkelstein, Donald Bashford

Journal:

Bioorganic & Medicinal Chemistry

Year:

2009

Language:

english

File:

PDF, 443 KB

english, 2009

33

Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculation

Bashford, Donald, Karplus, Martin

Journal:

Journal of Physical Chemistry

Year:

1991

Language:

english

File:

PDF, 661 KB

english, 1991

34

Ligand Binding Mode Prediction by Docking: Mdm2/Mdmx Inhibitors as a Case Study

Bharatham, Nagakumar, Bharatham, Kavitha, Shelat, Anang A., Bashford, Donald

Journal:

Journal of Chemical Information and Modeling

Year:

2014

Language:

english

File:

PDF, 3.48 MB

english, 2014

35

Identification and Characterization of an Allosteric Inhibitory Site on Dihydropteroate Synthase

Hammoudeh, Dalia I., Daté, Mihir, Yun, Mi-Kyung, Zhang, Weixing, Boyd, Vincent A., Viacava Follis, Ariele, Griffith, Elizabeth, Lee, Richard E., Bashford, Donald, White, Stephen W.

Journal:

ACS Chemical Biology

Year:

2014

Language:

english

File:

PDF, 3.65 MB

english, 2014

36

ChemInform Abstract: Generalized Born Models of Macromolecular Solvation Effects

Donald Bashford, David A. Case

Journal:

Year:

2001

File:

PDF, 24 KB

2001

37

Structural Details, Pathways, and Energetics of Unfolding Apomyoglobin

Alexey Onufriev, David A. Case, Donald Bashford

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 1.21 MB

english, 2003

38

Incorporating Protein Environments in Density Functional Theory: A Self-Consistent Reaction Field Calculation of Redox Potentials of [2Fe2S] Clusters in Ferredoxin and Phthalate Dioxygenase Reductase

Li, Jian, Nelson, Melanie R., Peng, Chun Y., Bashford, Donald, Noodleman, Louis

Journal:

Journal of Physical Chemistry A

Year:

1998

Language:

english

File:

PDF, 196 KB

english, 1998

39

Computational studies of the early intermediates of the bacteriorhodopsin photocycle

Michael Engels, Klaus Gerwert, Donald Bashford

Journal:

Biophysical Chemistry

Year:

1995

Language:

english

File:

PDF, 776 KB

english, 1995

40

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin

Donald Bashford, Klaus Gerwert

Journal:

Journal of Molecular Biology

Year:

1992

Language:

english

File:

PDF, 1.84 MB

english, 1992

41

The Major Secreted Product of the Whipworm, Trichuris, is a Pore-Forming Protein

Lesley Drake, Yuri Korchev, Lindsay Bashford, Mustafa Djamgoz, Derek Wakelin, Frank Ashall and Donald Bundy

Journal:

Proceedings Biological Sciences

Year:

1994

Language:

english

File:

PDF, 953 KB

english, 1994

42

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

Blachly, Patrick G., Sandala, Gregory M., Giammona, Debra Ann, Liu, Tiqing, Bashford, Donald, McCammon, J. Andrew, Noodleman, Louis

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.44 MB

english, 2014

43

Analysis of the Active-Site Mechanism of Tyrosyl-DNA Phosphodiesterase I: A Member of the Phospholipase D Superfamily

Stefan Gajewski, Evan Q. Comeaux, Nauzanene Jafari, Nagakumar Bharatham, Donald Bashford, Stephen W. White, Robert C.A.M. van Waardenburg

Journal:

Journal of Molecular Biology

Year:

2012

Language:

english

File:

PDF, 1.56 MB

english, 2012

44

A Fluid Salt-bridging Cluster and the Stabilization of p53

Thu Zar Lwin, Jason J. Durant, Donald Bashford

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.35 MB

english, 2007

45

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

Bashford, Donald, Karplus, Martin

Journal:

Year:

1990

Language:

english

File:

PDF, 1.69 MB

english, 1990

46

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

Blachly, Patrick G., Sandala, Gregory M., Giammona, Debra Ann, Bashford, Donald, McCammon, J. Andrew, Noodleman, Louis

Journal:

Inorganic Chemistry

Year:

2015

Language:

english

File:

PDF, 2.19 MB

english, 2015

47

Corrigendum to “Analysis of the Active-Site Mechanism of Tyrosyl-DNA Phosphodiesterase I: A Member of the Phospholipase D Superfamily” [J. Mol. Biol. 415/4 (2012) 741–758]

Stefan Gajewski, Evan Q. Comeaux, Nauzanene Jafari, Nagakumar Bharatham, Donald Bashford, Stephen W. White, Robert C.A.M. van Waardenburg

Journal:

Journal of Molecular Biology

Year:

2012

Language:

english

File:

PDF, 82 KB

english, 2012

48

Calculation of Redox Potentials and p K a Values of Hydrated Transition Metal Cations by a Combined Density Functional and Continuum Dielectric Theory

Li, Jian, Fisher, Cindy L., Chen, Jun L., Bashford, Donald, Noodleman, Louis

Journal:

Inorganic Chemistry

Year:

1996

Language:

english

File:

PDF, 265 KB

english, 1996

49

Density functional calculations of redox potentials for FeS clusters including solvation effects

Jun Liang Chen, Jean-Marie Mouesca, Louis Noodleman, David A. Case, Donald Bashford

Journal:

Journal of Inorganic Biochemistry

Year:

1993

Language:

english

File:

PDF, 52 KB

english, 1993

50

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

Konecny, Robert, Li, Jian, Fisher, Cindy L., Dillet, Valerie, Bashford, Donald, Noodleman, Louis

Journal:

Inorganic Chemistry

Year:

1999

Language:

english

File:

PDF, 160 KB

english, 1999

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