Donald Hamelberg

发表

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

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

Editorial

Donald Hamelberg, Wentian Li, 2020, Computational Biology and Chemistry.

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

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

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..

Elucidating Allosteric Communications in Proteins with Difference Contact Network Analysis

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

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

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

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

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

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.

An Empirical Study of the Universal Chemical Key Algorithm for Assigning Unique Keys to Chemical Compounds

Robert L. Grossman, Bing Liu, Donald Hamelberg, 2004, J. Bioinform. Comput. Biol..

Automatic Partition of Protein Molecular Dynamics using Coupled Hidden Markov-Ising Models

Donald Hamelberg, Ka Chun Ho, 2020 .

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..

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.

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.

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.

On the application of accelerated molecular dynamics to liquid water simulations.

Donald Hamelberg, J Andrew McCammon, César Augusto F de Oliveira, 2006, The journal of physical chemistry. B.

Chapter 12 Accelerating Conformational Transitions in Biomolecular Simulations

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

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.

Characterization of a novel DNA minor-groove complex.

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

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.

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

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

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.

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.

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

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

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.

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

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

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 .

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

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

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.

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

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

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.

Enhanced molecular dynamics sampling of drug target conformations

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

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

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

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.

Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease.

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

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

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