D. Hamelberg

发表

Sampling of slow diffusive conformational transitions with accelerated molecular dynamics.

J. Mccammon, D. Hamelberg, C. D. de Oliveira, 2007, The Journal of chemical physics.

Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1.

D. Hamelberg, Arghya Barman, 2016, The journal of physical chemistry. B.

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

Donald Hamelberg, E. Eisenmesser, D. Hamelberg, 2016, Proceedings of the National Academy of Sciences.

Atomistic basis for the on–off signaling mechanism in SAM-II riboswitch

Donald Hamelberg, D. Hamelberg, J. M. Kelley, 2009, Nucleic acids research.

Intricacies of interactions, dynamics and solvent effects in enzyme catalysis: a computational perspective on cyclophilin A

D. Hamelberg, Safieh Tork Ladani, 2014 .

The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain

Donald Hamelberg, Tongye Shen, Chenghang Zong, 2005, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.

J. Mongan, J. Mccammon, D. Hamelberg, 2004, The Journal of chemical physics.

Reoptimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics.

D. Hamelberg, U. Doshi, 2009, The journal of physical chemistry. B.

Conformational selection in the recognition of phosphorylated substrates by the catalytic domain of human Pin1.

D. Hamelberg, Hector A Velazquez, 2011, Biochemistry.

Entropic and surprisingly small intramolecular polarization effects in the mechanism of cyclophilin A.

D. Hamelberg, Safieh Tork Ladani, 2012, The journal of physical chemistry. B.

Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method.

Donald Hamelberg, J Andrew McCammon, J. Mccammon, 2004, Journal of the American Chemical Society.

DNA sequence dependent monomer-dimer binding modulation of asymmetric benzimidazole derivatives.

Donald Hamelberg, Christian Bailly, C. Bailly, 2004, Journal of the American Chemical Society.

The dilemma of conformational dynamics in enzyme catalysis: perspectives from theory and experiment.

D. Hamelberg, U. Doshi, 2014, Advances in experimental medicine and biology.

Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions.

D. Hamelberg, U. Doshi, 2012, Journal of chemical theory and computation.

Accelerated entropy estimates with accelerated dynamics.

David D. L. Minh, J. Mccammon, D. Hamelberg, 2007, The Journal of chemical physics.

Oscillatory Diffusion and Second-Order Cyclostationarity in Alanine Tripeptide from Molecular Dynamics Simulation.

Ka Chun Ho, D. Hamelberg, K. C. Ho, 2016, Journal of chemical theory and computation.

Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies.

D. Hamelberg, W. Wilson, L. Williams, 2002, Nucleic acids research.

Structural selectivity of aromatic diamidines.

J. Chaires, D. Hamelberg, W. Wilson, 2004, Journal of medicinal chemistry.

Synergistic mutations in soluble guanylyl cyclase (sGC) reveal a key role for interfacial regions in the sGC activation mechanism

Xin-Qiu Yao, D. Hamelberg, E. Garcin, 2019, The Journal of Biological Chemistry.

Clicking 1,2,4,5-tetrazine and cyclooctynes with tunable reaction rates.

D. Hamelberg, B. Wang, Danzhu Wang, 2012, Chemical communications.

Identification of an l-Phenylalanine Binding Site Enhancing the Cooperative Responses of the Calcium-sensing Receptor to Calcium*

Jenny J. Yang, E. Brown, D. Hamelberg, 2014, The Journal of Biological Chemistry.

Structural Mechanism of Cooperative Regulation of Calcium-Sensing Receptor-Mediated Cellular Signaling.

Jenny J. Yang, D. Hamelberg, K. Moremen, 2020, Current opinion in physiology.

Computational benchmarking of putative KIFC1 inhibitors

D. Hamelberg, R. Aneja, Nivya Sharma, 2022, Medicinal research reviews.

Cysteine-mediated dynamic hydrogen-bonding network in the active site of Pin1.

D. Hamelberg, Arghya Barman, 2014, Biochemistry.

Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove.

C. Bailly, D. Hamelberg, S. Neidle, 2002, Journal of the American Chemical Society.

Synthesis and effect of heterocycle modification on the spectroscopic properties of a series of unsymmetrical trimethine cyanine dyes

D. Hamelberg, Andrew Levitz, M. Henary, 2014 .

Role of F357 as an Oxygen Gate in the Oxidative Half-Reaction of Choline Oxidase.

D. Hamelberg, F. Salvi, G. Gadda, 2016, Biochemistry.

Design, synthesis and biological evaluation of di-substituted noscapine analogs as potent and microtubule-targeted anticancer agents.

D. Hamelberg, V. Tandon, R. Aneja, 2015, Bioorganic & medicinal chemistry letters.

Post-translational Modifications of Cyclophilin D Fine-Tune Its Conformational Dynamics and Activity: Implications for Its Mitochondrial Function

Xin-Qiu Yao, D. Hamelberg, Jacques Kumutima, 2022, The Journal of Physical Chemistry B.

Characterization of a novel DNA minor-groove complex.

Binh Nguyen, Stephen Neidle, Donald Hamelberg, 2004, Biophysical journal.

High-pressure effect on the dynamics of solvated peptides.

Ricky B. Nellas, D. Hamelberg, T. Shen, 2012, The Journal of chemical physics.

Donor acceptor fluorophores: synthesis, optical properties, TD-DFT and cytotoxicity studies.

D. Hamelberg, R. Aneja, M. Henary, 2021, Organic & biomolecular chemistry.

Molecular cycloencapsulation augments solubility and improves therapeutic index of brominated noscapine in prostate cancer cells.

D. Hamelberg, V. Rangari, R. Aneja, 2012, Molecular pharmaceutics.

Flexible Structure of DNA: Ion Dependence of Minor-Groove Structure and Dynamics

Donald Hamelberg, W. David Wilson, D. Hamelberg, 2000 .

Extracellular Calcium Modulates Actions of Orthosteric and Allosteric Ligands on Metabotropic Glutamate Receptor 1α*

Jenny J. Yang, E. Brown, D. Hamelberg, 2013, The Journal of Biological Chemistry.

Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis-trans isomerases.

D. Hamelberg, Arghya Barman, Safieh Tork Ladani, 2015, Biochimica et biophysica acta.

Mechanistic Insight into the Role of Transition-State Stabilization in Cyclophilin A

J. Mccammon, D. Hamelberg, J. McCammon, 2008, Journal of the American Chemical Society.

Enhanced molecular dynamics sampling of drug target conformations

Donald Hamelberg, D. Hamelberg, U. Doshi, 2016, Biopolymers.

Novel third-generation water-soluble noscapine analogs as superior microtubule-interfering agents with enhanced antiproliferative activity.

Eric A. Owens, D. Hamelberg, V. Tandon, 2014, Biochemical pharmacology.

Cyclodextrin Complexes of Reduced Bromonoscapine in Guar Gum Microspheres Enhance Colonic Drug Delivery

D. Hamelberg, V. Rangari, R. Aneja, 2014, Molecular pharmaceutics.

The role of conserved water molecules in the catalytic domain of protein kinases

Donald Hamelberg, J Andrew McCammon, James D R Knight, 2009, Proteins.

Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch.

Donald Hamelberg, D. Hamelberg, U. Doshi, 2012, RNA.

A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw

Donald Hamelberg, J Andrew McCammon, Tongye Shen, 2007, Proceedings of the National Academy of Sciences.

Second Generation G-Quadruplex Stabilizing Trimethine Cyanines.

Eric A. Owens, D. Hamelberg, W. Wilson, 2019, Bioconjugate chemistry.

Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme.

Donald Hamelberg, D. Hamelberg, Yao Xin, 2010, RNA.

Conformational plasticity of an enzyme during catalysis: intricate coupling between cyclophilin A dynamics and substrate turnover.

D. Hamelberg, L. McGowan, 2013, Biophysical journal.

Resolving the complex role of enzyme conformational dynamics in catalytic function

Donald Hamelberg, D. Hamelberg, U. Doshi, 2012, Proceedings of the National Academy of Sciences.

Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study.

Donald Hamelberg, J Andrew McCammon, J. Mccammon, 2007, The Journal of chemical physics.

Detecting Functional Dynamics in Proteins with Comparative Perturbed-Ensembles Analysis.

Xin-Qiu Yao, Donald Hamelberg, Xin-Qiu Yao, 2019, Accounts of chemical research.

Combinatorial Coarse-Graining of Molecular Dynamics Simulations for Detecting Relationships between Local Configurations and Overall Conformations.

Donald Hamelberg, Ka Chun Ho, D. Hamelberg, 2018, Journal of chemical theory and computation.

Elucidating Allosteric Communications in Proteins with Difference Contact Network Analysis

Xin-Qiu Yao, Donald Hamelberg, Mohamed Momin, 2018, J. Chem. Inf. Model..

Unraveling Allosteric Mechanisms of Enzymatic Catalysis with an Evolutionary Analysis of Residue–Residue Contact Dynamical Changes

Xin-Qiu Yao, Donald Hamelberg, Xin-Qiu Yao, 2018 .

A statistical analysis of the precision of reweighting-based simulations.

Donald Hamelberg, Tongye Shen, D. Hamelberg, 2008, The Journal of chemical physics.

Subsets of adjacent nodes (SOAN): a fast method for computing suboptimal paths in protein dynamic networks

Xin-Qiu Yao, Donald Hamelberg, Thomas Dodd, 2021, Molecular Physics.

Solvent-Slaved Motions in the Hydride Tunneling Reaction Catalyzed by Human Glycolate Oxidase

D. Hamelberg, G. Gadda, Safieh Tork Ladani, 2016 .

Non-active Site Residue in Loop L4 Alters Substrate Capture and Product Release in d-Arginine Dehydrogenase

Xin-Qiu Yao, D. Hamelberg, G. Gadda, 2023, Biochemistry.

Decoding Allosteric Communication Pathways in Cyclophilin A with a Comparative Analysis of Perturbed Conformational Ensembles.

Xin-Qiu Yao, D. Hamelberg, Isela Rodriguez-Bussey, 2018, The journal of physical chemistry. B.

A dry ligand-binding cavity in a solvated protein

D. Hamelberg, B. Halle, Johan Qvist, 2008, Proceedings of the National Academy of Sciences.

Substrate Sequence Determines Catalytic Activities, Domain-Binding Preferences, and Allosteric Mechanisms in Pin1.

Xin-Qiu Yao, D. Hamelberg, Mohamed Momin, 2018, The journal of physical chemistry. B.

Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins

Donald Hamelberg, Arghya Barman, Crystal Smitherman, 2016, J. Chem. Inf. Model..

Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations.

D. Hamelberg, Hector A Velazquez, 2015, The Journal of chemical physics.

Conformation-directed catalysis and coupled enzyme-substrate dynamics in Pin1 phosphorylation-dependent cis-trans isomerase.

D. Hamelberg, Hector A Velazquez, 2013, The journal of physical chemistry. B.

Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH···π Interactions in Proteins.

D. Hamelberg, Arghya Barman, B. Batiste, 2015, Journal of chemical theory and computation.

Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self‐association of cis–tau peptide

D. Hamelberg, Arghya Barman, 2015, Proteins.

Insight into the role of hydration on protein dynamics.

J. Mccammon, D. Hamelberg, T. Shen, 2006, The Journal of chemical physics.

Tuning Protein Dynamics to Sense Rapid Endoplasmic Reticulum Calcium Dynamics.

Jenny J. Yang, Xin-Qiu Yao, D. Hamelberg, 2021, Angewandte Chemie.

Fe(II)/Fe(III) Redox Process Can Significantly Modulate the Conformational Dynamics and Electrostatics of Pirin in NF-κB Regulation

D. Hamelberg, Arghya Barman, 2016, ACS Omega.

Role of Ca2+ and L-Phe in Regulating Functional Cooperativity of Disease- Associated â•Ÿâ•ŸToggleâ•Žâ•Ž Calcium-Sensing Receptor Mutations

Jenny J. Yang, E. Brown, D. Hamelberg, 2020 .

Role of Ca2+ and L-Phe in Regulating Functional Cooperativity of Disease-Associated “Toggle” Calcium-Sensing Receptor Mutations

Jenny J. Yang, E. Brown, D. Hamelberg, 2014, PloS one.

Establishing a Framework of Using Residue-Residue Interactions in Protein Difference Network Analysis

Xin-Qiu Yao, Donald Hamelberg, Mohamed Momin, 2019, J. Chem. Inf. Model..

Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design

Donald Hamelberg, Mulpuri Nagaraju, Lauren C. McGowan, 2013, J. Chem. Inf. Model..

Protein conformational dynamics in the mechanism of HIV-1 protease catalysis

W. M. Westler, S. Kent, D. Hamelberg, 2011, Proceedings of the National Academy of Sciences.

Residue-Residue Contact Changes during Functional Processes Define Allosteric Communication Pathways.

Xin-Qiu Yao, D. Hamelberg, 2022, Journal of chemical theory and computation.

N-Glycosylation and Gaucher Disease Mutation Allosterically Alter Active-Site Dynamics of Acid-β-Glucosidase

Xin-Qiu Yao, D. Hamelberg, Mohamed Momin, 2020 .

A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity.

I. Weber, D. Hamelberg, A. Iyer, 2021, Biochemistry.

Enzyme-Mediated Conversion of Flavin Adenine Dinucleotide (FAD) to 8-Formyl FAD in Formate Oxidase Results in a Modified Cofactor with Enhanced Catalytic Properties.

D. Hamelberg, A. Bommarius, G. Gadda, 2017, Biochemistry.

Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers' Theory.

D. Hamelberg, U. Doshi, 2011, Journal of chemical theory and computation.

Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects.

W D Wilson, D. Hamelberg, W. Wilson, 2001, Journal of the American Chemical Society.

Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics.

Donald Hamelberg, D. Hamelberg, U. Doshi, 2015, Biochimica et biophysica acta.

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.

D. Hamelberg, U. Doshi, 2014, The journal of physical chemistry letters.

Insights on the mechanism of amine oxidation catalyzed by D-arginine dehydrogenase through pH and kinetic isotope effects.

D. Hamelberg, G. Gadda, Hongling Yuan, 2011, Journal of the American Chemical Society.

From Distinct to Differential Conformational Dynamics to Map Allosteric Communication Pathways in Proteins.

Xin-Qiu Yao, D. Hamelberg, 2022, The journal of physical chemistry. B.

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

César Augusto F. de Oliveira, J. Andrew McCammon, Donald Hamelberg, 2008, Journal of chemical theory and computation.

Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis.

Donald Hamelberg, J Andrew McCammon, Tongye Shen, 2005, Journal of the American Chemical Society.

Redox-Specific Allosteric Modulation of the Conformational Dynamics of κB DNA by Pirin in the NF-κB Supramolecular Complex.

D. Hamelberg, Charles A. Adeniran, 2017, Biochemistry.

Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism.

J. Mccammon, D. Hamelberg, B. Schiøtt, 2007, Biopolymers.

Chapter 12 Accelerating Conformational Transitions in Biomolecular Simulations

J. Andrew McCammon, Donald Hamelberg, J. Mccammon, 2006 .

Mapping the tropomyosin isoform 5 binding site on human erythrocyte tropomodulin: further insights into E-Tmod/TM5 interaction.

D. Hamelberg, J. Lao, L. Sung, 2005, Archives of biochemistry and biophysics.

Experimental studies of the universal chemical key (UCK) algorithm on the NCI database of chemical compounds

Robert L. Grossman, Bing Liu, Donald Hamelberg, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Conserved Conformational Dynamics Reveal a Key Dynamic Residue in the Gatekeeper Loop of Human Cyclophilins.

Xin-Qiu Yao, D. Hamelberg, Furyal Ahmed, 2023, The journal of physical chemistry. B.

An Iron Reservoir to the Catalytic Metal

D. Hamelberg, Arghya Barman, A. Ozarowski, 2015, The Journal of Biological Chemistry.

Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase.

D. Hamelberg, G. Gadda, Daniel Ouedraogo, 2017, Biochemistry.

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

J. Andrew McCammon, Donald Hamelberg, Mikolai Fajer, 2008, Journal of chemical theory and computation.

Extracellular Calcium Modulates Actions of Orthosteric and Allosteric Ligands on Metabotropic Glutamate Receptor 1α*

Jenny J. Yang, D. Hamelberg, P. Conn, 2013, The Journal of Biological Chemistry.

Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations.

Donald Hamelberg, Tongye Shen, D. Hamelberg, 2005, The Journal of chemical physics.

Examining the limits of time reweighting and Kramers' rate theory to obtain correct kinetics from accelerated molecular dynamics.

D. Hamelberg, U. Doshi, Yao Xin, 2010, The Journal of chemical physics.

Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective.

D. Hamelberg, Mohamed Momin, Yao Xin, 2017, The journal of physical chemistry. B.