D. Bashford

发表

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

A. Lesk, C. Chothia, D. Bashford, 1987, Journal of molecular biology.

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

Alexander D. MacKerell, M. Karplus, D. Nguyen, 1998, The journal of physical chemistry. B.

Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility.

Tony J. You, D. Bashford, T. You, 1995, Biophysical journal.

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

D. Bashford, K. Gerwert, 1992, Journal of molecular biology.

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

M. Karplus, D. Bashford, 1991 .

Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin

D. Bashford, K. Gerwert, 1992 .

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

M. Karplus, D. Bashford, 1990, Biochemistry.

Generalized Born Models of Macromolecular Solvation Effects

D. Case, D. Bashford, 2001 .

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

D. Case, D. Bashford, A. Onufriev, 2004, Proteins.

Generalized born models of macromolecular solvation effects.

D. Case, D. Bashford, 2000, Annual review of physical chemistry.

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

Donald Bashford, D. Bashford, Thu Zar Lwin, 2007, Journal of molecular biology.

Implicit Solvent Electrostatics in Biomolecular Simulation

Nathan A. Baker, David A. Case, Donald Bashford, 2006 .

Macroscopic electrostatic models for protonation states in proteins.

Donald Bashford, D. Bashford, 2004, Frontiers in bioscience : a journal and virtual library.

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

D. Bashford, V. Spassov, 1999 .

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

D. Bashford, V. Spassov, D Bashford, 1998, Protein science : a publication of the Protein Society.

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

P E Wright, D. Case, D. Bashford, 1993, Biochemistry.

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

D. Bashford, K. Gerwert, H. Luecke, 2001, Journal of molecular biology.

Density functional theory analysis of structure, energetics, and spectroscopy for the Mn-Fe active site of Chlamydia trachomatis ribonucleotide reductase in four oxidation states.

D. Bashford, W. Han, Louis Noodleman, 2010, Inorganic chemistry.

Modification of the Generalized Born Model Suitable for Macromolecules

D. Case, D. Bashford, A. Onufriev, 2000 .

Use of 1H NMR spectroscopy and computer simulations To analyze histidine pKa changes in a protein tyrosine phosphatase: experimental and theoretical determination of electrostatic properties in a small protein.

D. Bashford, P. Tishmack, E. Harms, 1997, Biochemistry.

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

D. Bashford, Tiqing Liu, Louis Noodleman, 2002, Journal of the American Chemical Society.

Absolute pKa calculations with continuum dielectric methods

Carmay Lim, Martin Karplus, M. Karplus, 1991 .

DENSITY FUNCTIONAL/POISSON-BOLTZMANN CALCULATIONS OF REDOX POTENTIALS FOR IRON-SULFUR CLUSTERS

David A. Case, Donald Bashford, Jun L. Chen, 1994 .

Incorporating solvation effects into density functional electronic structure calculations

David A. Case, Donald Bashford, Jun L. Chen, 1994 .

Incorporating solvation effects into density functional theory: Calculation of absolute acidities

D. Case, D. Bashford, W. Richardson, 1997 .

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

D. Bashford, H. Dyson, D Bashford, 1998, Biochemistry.

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

Donald Bashford, Alexey Onufriev, D. Bashford, 2003, Journal of molecular biology.

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

D. Bashford, E. Getzoff, E. Demchuk, 2000, Biochemistry.

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

Donald Bashford, D. Bashford, Valerie Dillet, 2000 .

Monitoring Ligand-Induced Protein Ordering in Drug Discovery.

D. Bashford, M. Dyer, R. Kriwacki, 2016, Journal of molecular biology.

Identification and Characterization of an Allosteric Inhibitory Site on Dihydropteroate Synthase

D. Bashford, D. Hammoudeh, S. White, 2014, ACS chemical biology.

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

D. Bashford, D. Finkelstein, M. Krishnamurthy, 2009, Bioorganic & medicinal chemistry.

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

Maria C. Nagan, D. Bashford, J. Gelpí, 2002, RNA.

First Small Molecule Inhibitor of MDMX Identification and Characterization of the Cell Biology :

Anang A. Shelat, Michael A. Dyer, Donald Bashford, 2010 .

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

Patrick G. Blachly, J. Mccammon, D. Bashford, 2015, Inorganic chemistry.

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

M. Loh, C. Pui, W. Evans, 2014 .

Liu F-NMR 19 by-Adrenergic Receptor Characterized 2 β Biased Signaling Pathways in

D. Bashford, S. White, Richard E. Lee, 2012 .

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

D. Bashford, N. Mahindroo, N. Fujii, 2008, Bioorganic & medicinal chemistry letters.

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

D. Bashford, N. Bharatham, S. White, 2012, Journal of molecular biology.

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

K. Hahn, D. Bashford, Tiqing Liu, 2007, The journal of physical chemistry. A.

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

D. Bashford, Louis Noodleman, Jian Li, 1999, Inorganic chemistry.

Model for proton transport coupled to protein conformational change: application to proton pumping in the bacteriorhodopsin photocycle.

D. Bashford, Antonio M. Ferreira, 2006, Journal of the American Chemical Society.

Catalysis and Sulfa Drug Resistance in Dihydropteroate Synthase

D. Bashford, M. B. Waddell, S. White, 2012, Science.

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

D. Bashford, Louis Noodleman, Jian Li, 1999, Inorganic chemistry.

Identification and Characterization of the First Small Molecule Inhibitor of MDMX*

D. Bashford, A. Shelat, A. Jochemsen, 2010, The Journal of Biological Chemistry.

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

K. Hahn, D. Bashford, Tiqing Liu, 2003, Chemphyschem : a European journal of chemical physics and physical chemistry.

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.

D. Bashford, W. Han, Louis Noodleman, 2011, Dalton transactions.

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

M. Loh, M. Relling, C. Pui, 2014, Blood.

Electrostatic effects in biological molecules

D. Bashford, 1991 .

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

M. Karplus, D. Bashford, Sangyoub Lee, 1987, Biopolymers.

Diffusion‐collision model for the folding kinetics of myoglobin

I. Kuntz, M. Karplus, F. Cohen, 1988, Proteins.

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

Donald Bashford, D. Bashford, R. Kriwacki, 2005, Journal of molecular biology.

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

Patrick G. Blachly, J. Mccammon, D. Bashford, 2014, Journal of chemical theory and computation.

Unimolecular diffusion‐mediated reactions with a nonrandom time‐modulated absorbing barrier

D. Bashford, D. Weaver, 1986 .

Structural details, pathways, and energetics of unfolding apomyoglobin.

Donald Bashford, David A Case, Alexey Onufriev, 2003, Journal of molecular biology.

STRUCTURE AND DYNAMICS OF SELF-ASSEMBLING PEPTIDE NANOTUBES AND THE CHANNEL-MEDIATED WATER ORGANIZATION AND SELF-DIFFUSION. A MOLECULAR DYNAMICS STUDY

Donald Bashford, D. Bashford, M. Ghadiri, 1995 .

Computational studies of the early intermediates of the bacteriorhodopsin photocycle.

D. Bashford, K. Gerwert, M. Engels, 1995, Biophysical chemistry.

Photoisomerization and proton transfer in photoactive yellow protein.

D. Bashford, E. Getzoff, Louis Noodleman, 2003, Journal of the American Chemical Society.

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

M. Karplus, D. Bashford, G. Canters, 1988, Journal of molecular biology.

Macroscopic Electrostatics: Calculation of Solvated Interactions and Macromolecular Titration

D. Bashford, 2002 .

An Object-Oriented Programming Suite for Electrostatic Effects in Biological Molecules

Donald Bashford, D. Bashford, 1997, ISCOPE.

Incomplete Folding upon Binding Mediates Cdk4/Cyclin D Complex Activation by Tyrosine Phosphorylation of Inhibitor p27 Protein*

D. Bashford, R. Kriwacki, S. Otieno, 2011, The Journal of Biological Chemistry.

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

Anang A. Shelat, Donald Bashford, Kavitha Bharatham, 2014, J. Chem. Inf. Model..

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

D. Case, G. Gippert, D. Bashford, 1997, Journal of molecular biology.

A computational study of the role of solvation effects in reverse turn formation in the tetrapeptides APGD and APGN

David A. Case, Donald Bashford, D. Case, 1997 .

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

David A. Case, Alexey Onufriev, Donald Bashford, 2002, J. Comput. Chem..

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

Donald Bashford, Velin Z. Spassov, D. Bashford, 1999, J. Comput. Chem..

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

Donald Bashford, R Kiplin Guy, Nagakumar Bharatham, 2017, Journal of molecular graphics & modelling.

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

K. Hahn, D. Bashford, Tiqing Liu, 2004 .

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

D. Case, D. Bashford, D Bashford, 1997, Folding & design.

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

D. Case, D. Bashford, Louis Noodleman, 1993 .

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

D. Bashford, K. Gerwert, H. Luecke, 2001, Journal of molecular biology.

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

D. Bashford, D Bashford, N Arora, 2001, Proteins.

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

D. Bashford, D. Asthagiri, D Asthagiri, 2002, Biophysical journal.

Dielectric Continuum Models for Hydration Effects on Peptide Conformational Transitions

Charles L. Brooks, David A. Case, Donald Bashford, 1996 .

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, Tony J. You, 1995, J. Comput. Chem..

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

Donald Bashford, David L. Weaver, Martin Karplus, 1984 .