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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

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

3

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

4

Macroscopic electrostatic models for protonation states in proteins

Bashford, Donald

Journal:

Frontiers in Bioscience

Year:

2004

Language:

english

File:

PDF, 444 KB

english, 2004

5

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

6

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

7

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

8

ChemInform Abstract: Generalized Born Models of Macromolecular Solvation Effects

Donald Bashford, David A. Case

Journal:

Year:

2001

File:

PDF, 24 KB

2001

9

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

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

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

12

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

13

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

14

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

15

Diffusion-collision model for the folding kinetics of myoglobin

Dr. Donald Bashford, F. E. Cohen, M. Karplus, I. D. Kuntz, D. L. Weaver

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1988

Language:

english

File:

PDF, 1.24 MB

english, 1988

16

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

17

Density-Functional and Electrostatic Calculations for a Model of a Manganese Superoxide Dismutase Active Site in Aqueous Solution

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

Journal:

Journal of Physical Chemistry

Year:

1996

Language:

english

File:

PDF, 640 KB

english, 1996

18

GENERALIZED BORN MODELS OF MACROMOLECULAR SOLVATION EFFECTS

Bashford, Donald, Case, David A.

Journal:

Annual Review of Physical Chemistry

Year:

2000

Language:

english

File:

PDF, 209 KB

english, 2000

19

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

20

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

21

pKa calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin

Velin Z Spassov, Hartmut Luecke, Klaus Gerwert, Donald Bashford

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 478 KB

english, 2001

22

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

23

Disordered p27Kip1 Exhibits Intrinsic Structure Resembling the Cdk2/Cyclin A-bound Conformation

Sivashankar G. Sivakolundu, Donald Bashford, Richard W. Kriwacki

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 884 KB

english, 2005

24

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

25

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

26

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

27

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

28

Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle

Alexey Onufriev, Alexander Smondyrev, Donald Bashford

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 1.11 MB

english, 2003

29

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

30

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

31

Density Functional/Poisson-Boltzmann Calculations of Redox Potentials for Iron-Sulfur Clusters

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

Journal:

Journal of the American Chemical Society

Year:

1994

Language:

english

File:

PDF, 2.02 MB

english, 1994

32

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

33

Electrostatic calculations of side-chain pKa values in myoglobin and comparison with NMR data for histidines

Bashford, Donald, Case, David A., Dalvit, Claudio, Tennant, Linda, Wright, Peter E.

Journal:

Year:

1993

Language:

english

File:

PDF, 2.02 MB

english, 1993

34

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

35

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

36

Electrostatic effects in biological molecules

Bashford, Donald

Journal:

Current Opinion in Structural Biology

Year:

1991

Language:

english

File:

PDF, 1.09 MB

english, 1991

37

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

38

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

39

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

40

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

41

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

42

Density Functional Study of the Mechanism of a Tyrosine Phosphatase: I. Intermediate Formation

Asthagiri, Dilipkumar, Dillet, Valerie, Liu, Tiqing, Noodleman, Louis, Van Etten, Robert L., Bashford, Donald

Journal:

Journal of the American Chemical Society

Year:

2002

Language:

english

File:

PDF, 206 KB

english, 2002

43

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

44

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

45

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

46

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

47

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

48

Density Functional Theory Analysis of Structure, Energetics, and Spectroscopy for the Mn−Fe Active Site of Chlamydia trachomatis Ribonucleotide Reductase in Four Oxidation States

Han, Wen-Ge, Giammona, Debra Ann, Bashford, Donald, Noodleman, Louis

Journal:

Inorganic Chemistry

Year:

2010

Language:

english

File:

PDF, 4.63 MB

english, 2010

49

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

50

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