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1

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules

Hamelberg, Donald, Mongan, John, McCammon, J. Andrew

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 1.93 MB

english, 2004

2

Enhanced smolt characteristics of steelhead trout exposed to alternative hatchery conditions during the final months of rearing

Gayle B. Zydlewski, J.Scott Foott, Kenneth Nichols, Scott Hamelberg, Joseph Zydlewski, Björn Thrandur Björnsson

Journal:

Year:

2003

Language:

english

File:

PDF, 238 KB

english, 2003

3

Effective Population Size in Winter-Run Chinook Salmon

Philip W. Hedrick, Dennis Hedgecock, Scott Hamelberg

Journal:

Conservation Biology

Year:

1995

Language:

english

File:

PDF, 773 KB

english, 1995

4

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

Jiang, J. Y., Nagaraju, M., Meyer, R. C., Zhang, L., Hamelberg, D., Hall, R. A., Brown, E. M., Conn, P. J., Yang, J. J.

Journal:

Journal of Biological Chemistry

Year:

2014

Language:

english

File:

PDF, 3.03 MB

english, 2014

5

Detecting Functional Dynamics in Proteins with Comparative Perturbed-Ensembles Analysis

Yao, Xin-Qiu, Hamelberg, Donald

Journal:

Accounts of Chemical Research

Year:

2019

File:

PDF, 4.83 MB

2019

6

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

Jesper Sørensen, Donald Hamelberg, Birgit Schiøtt, J. Andrew McCammon

Journal:

Year:

2007

Language:

english

File:

PDF, 502 KB

english, 2007

7

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

James D. R. Knight, Donald Hamelberg, J. Andrew McCammon, Rashmi Kothary

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 355 KB

english, 2009

8

Conformational Selection in the Recognition of Phosphorylated Substrates by the Catalytic Domain of Human Pin1

Velazquez, Hector A., Hamelberg, Donald

Journal:

Year:

2011

Language:

english

File:

PDF, 5.71 MB

english, 2011

9

Resolving the complex role of enzyme conformational dynamics in catalytic function

Doshi, U., McGowan, L. C., Ladani, S. T., Hamelberg, D.

Journal:

Proceedings of the National Academy of Sciences

Year:

2012

Language:

english

File:

PDF, 3.40 MB

english, 2012

10

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

Chen, Weixuan, Wang, Danzhu, Dai, Chaofeng, Hamelberg, Donald, Wang, Binghe

Journal:

Chemical Communications

Year:

2012

Language:

english

File:

PDF, 2.49 MB

english, 2012

11

Molecular Cycloencapsulation Augments Solubility and Improves Therapeutic Index of Brominated Noscapine in Prostate Cancer Cells

Madan, Jitender, Baruah, Bharat, Nagaraju, Mulpuri, Abdalla, Mohamed O., Yates, Clayton, Turner, Timothy, Rangari, Vijay, Hamelberg, Donald, Aneja, Ritu

Journal:

Molecular Pharmaceutics

Year:

2012

Language:

english

File:

PDF, 2.59 MB

english, 2012

12

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

Carlos Vera, Jianmin Lao, Donald Hamelberg, Lanping Amy Sung

Journal:

Archives of Biochemistry and Biophysics

Year:

2005

Language:

english

File:

PDF, 483 KB

english, 2005

13

Influence of the Dynamic Positions of Cations on the Structure of the DNA Minor Groove: Sequence-Dependent Effects

Hamelberg, Donald, Williams, Loren Dean, Wilson, W. David

Journal:

Journal of the American Chemical Society

Year:

2001

Language:

english

File:

PDF, 313 KB

english, 2001

14

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

Hamelberg, Donald, McFail-Isom, Lori, Williams, Loren Dean, Wilson, W. David

Journal:

Journal of the American Chemical Society

Year:

2000

Language:

english

File:

PDF, 305 KB

english, 2000

15

Post-spawn migrations of hatchery-originOncorhynchus mykisskelts in the Central Valley of California

Robert E. Null,Kevin S. Niemela,Scott F. Hamelberg

Journal:

Environmental Biology of Fishes

Year:

2013

Language:

english

File:

PDF, 1.67 MB

english, 2013

16

Characterization of a Novel DNA Minor-Groove Complex

Nguyen, Binh, Hamelberg, Donald, Bailly, Christian, Colson, Pierre, Stanek, Jaroslav, Brun, Reto, Neidle, Stephen, David Wilson, W.

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 491 KB

english, 2004

17

A manual of anaesthetic techniques: By William J. Pryor, m.b., ch.b., f.f.a.r.c.s. 228 pages. John Wright & Sons, Ltd. Bristol, Eng. 1959. $7.00

William Hamelberg

Journal:

The American Journal of Surgery

Year:

1960

Language:

english

File:

PDF, 103 KB

english, 1960

18

A synopsis of anaesthesia: By J. Alfred Lee, m.r.c.s., l.r.c.p., m.m.s.a., f.f.a.r.c.s., d.a. Fourth edition, 616 pages. Williams & Wilkins Co. Baltimore, 1959. $6.50

William Hamelberg

Journal:

The American Journal of Surgery

Year:

1960

Language:

english

File:

PDF, 111 KB

english, 1960

19

Advances in anesthesiology: Muscle relaxants: Edited by Lester C. Mark, m.d. and E. M. Papper, m.d. First edition, vii + 118 pp., with tables and 35 figures. New York, 1967. Hoeber Medical Division of Harper and Row. $6.25

William Hamelberg

Journal:

The American Journal of Surgery

Year:

1968

Language:

english

File:

PDF, 91 KB

english, 1968

20

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

Nagaraju, Mulpuri, McGowan, Lauren C., Hamelberg, Donald

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 1.16 MB

english, 2013

21

[Annual Reports in Computational Chemistry] Volume 2 || Chapter 12 Accelerating Conformational Transitions in Biomolecular Simulations

Hamelberg, Donald

Year:

2006

Language:

english

File:

PDF, 203 KB

english, 2006

22

DNA Sequence Dependent Monomer−Dimer Binding Modulation of Asymmetric Benzimidazole Derivatives

Tanious, Farial A., Hamelberg, Donald, Bailly, Christian, Czarny, Agnieska, Boykin, David W., Wilson, W. David

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 501 KB

english, 2004

23

Conformation-Directed Catalysis and Coupled Enzyme–Substrate Dynamics in Pin1 Phosphorylation-Dependent Cis–Trans Isomerase

Velazquez, Hector A., Hamelberg, Donald

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 1.29 MB

english, 2013

24

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

Levitz, Andrew, Ladani, Safieh Tork, Hamelberg, Donald, Henary, Maged

Journal:

Dyes and Pigments

Year:

2014

Language:

english

File:

PDF, 1.81 MB

english, 2014

25

Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover

McGowan, Lauren C., Hamelberg, Donald

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 1.32 MB

english, 2013

26

Disease Related Mutations Adjacent to Predicted Multiple Ca2+ Binding Sites of Ca2+-Sensing Receptor Altering Intracellular Ca2+ Oscillations via Extracellular Calcium and Amino Acid Signaling

Zhang, Chen, Hannan, Fadil, Huang, Yun, Jiang, Yusheng, Nagaraju, Mulpuri, Thakker, Rajesh, Hamelberg, Donald, Brown, Edward, Yang, Jenny

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 42 KB

english, 2012

27

MCPH1 deletion in a newborn with severe microcephaly and premature chromosome condensation

Pfau, Ruthann B., Thrush, Devon Lamb, Hamelberg, Elizabeth, Bartholomew, Dennis, Botes, Shaun, Pastore, Matthew, Tan, Christopher, del Gaudio, Daniela, Gastier-Foster, Julie M., Astbury, Caroline

Journal:

European Journal of Medical Genetics

Year:

2013

Language:

english

File:

PDF, 756 KB

english, 2013

28

Fatigue damage analysis of notched carbon/epoxy composite by spate and finite element method

Pfau, Ruthann B., Thrush, Devon Lamb, Hamelberg, Elizabeth, Bartholomew, Dennis, Botes, Shaun, Pastore, Matthew, Tan, Christopher, del Gaudio, Daniela, Gastier-Foster, Julie M., Astbury, Caroline

Journal:

NDT & E International

Year:

1993

Language:

english

File:

PDF, 159 KB

english, 1993

29

Hetero Interaction with an Amino Acid Globally Enhances Cooperative Activation of CaSR in Response to Extracellular Signaling

Zhang, Chen, Zhuo, You, Feng, Jie, Strachan, Heather, Mulpuri, Nagaraju, Hamelberg, Donald, Moremen, Kelley, Brown, Edward M., Yang, Jenny J.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 85 KB

english, 2013

30

Cysteine-Mediated Dynamic Hydrogen-Bonding Network in the Active Site of Pin1

Barman, Arghya, Hamelberg, Donald

Journal:

Year:

2014

Language:

english

File:

PDF, 2.86 MB

english, 2014

31

The Cluster of Hydrophobic Residues Controls the Entrance to the Active Site of Choline Oxidase

Xin, Yao, Gadda, Giovanni, Hamelberg, Donald

Journal:

Year:

2009

Language:

english

File:

PDF, 3.01 MB

english, 2009

32

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

de Oliveira, César Augusto F., Hamelberg, Donald, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 1.92 MB

english, 2008

33

On the Application of Accelerated Molecular Dynamics to Liquid Water Simulations

de Oliveira, César Augusto F, Hamelberg, Donald, McCammon, J. Andrew

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 187 KB

english, 2006

34

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

Hamelberg, Donald, McCammon, J. Andrew

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 692 KB

english, 2009

35

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

Doshi, Urmi, Hamelberg, Donald

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 1.71 MB

english, 2011

36

Insights on the Mechanism of Amine Oxidation Catalyzed by d -Arginine Dehydrogenase Through pH and Kinetic Isotope Effects

Yuan, Hongling, Xin, Yao, Hamelberg, Donald, Gadda, Giovanni

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 1.19 MB

english, 2011

37

Entropic and Surprisingly Small Intramolecular Polarization Effects in the Mechanism of Cyclophilin A

Ladani, Safieh Tork, Hamelberg, Donald

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 3.76 MB

english, 2012

38

Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method

Hamelberg, Donald, McCammon, J. Andrew

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 186 KB

english, 2004

39

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

Henary, Maged, Narayana, Lakshminarayana, Ahad, Shazia, Gundala, Sushma R., Mukkavilli, Rao, Sharma, Vibhuti, Owens, Eric A., Yadav, Yogesh, Nagaraju, Mulpuri, Hamelberg, Donald, Tandon, Vibha, Panda,

Journal:

Biochemical Pharmacology

Year:

2014

Language:

english

File:

PDF, 2.69 MB

english, 2014

40

Water’s Contribution to the Energetic Roughness from Peptide Dynamics

Johnson, Quentin, Doshi, Urmi, Shen, Tongye, Hamelberg, Donald

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 2.82 MB

english, 2010

41

Phosphorylation Effects on cis/trans Isomerization and the Backbone Conformation of Serine−Proline Motifs: Accelerated Molecular Dynamics Analysis

Hamelberg, Donald, Shen, Tongye, McCammon, J. Andrew

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 371 KB

english, 2005

42

Reoptimization of the AMBER Force Field Parameters for Peptide Bond (Omega) Torsions Using Accelerated Molecular Dynamics

Doshi, Urmi, Hamelberg, Donald

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 822 KB

english, 2009

43

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent

Doshi, Urmi, Hamelberg, Donald

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 2.81 MB

english, 2014

44

Strong Binding in the DNA Minor Groove by an Aromatic Diamidine with a Shape That Does Not Match the Curvature of the Groove

Nguyen, Binh, Lee, Michael P. H., Hamelberg, Donald, Joubert, Alexandra, Bailly, Christian, Brun, Reto, Neidle, Stephen, Wilson, W. David

Journal:

Journal of the American Chemical Society

Year:

2002

Language:

english

File:

PDF, 137 KB

english, 2002

45

Fast Peptidyl cis−trans Isomerization within the Flexible Gly-Rich Flaps of HIV-1 Protease

Hamelberg, Donald, McCammon, J. Andrew

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 117 KB

english, 2005

46

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

Doshi, Urmi, Hamelberg, Donald

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 4.92 MB

english, 2012

47

Structural Selectivity of Aromatic Diamidines

Chaires, Jonathan B., Ren, Jinsong, Hamelberg, Donald, Kumar, Arvind, Pandya, Vandna, Boykin, David W., Wilson, W. David

Journal:

Journal of Medicinal Chemistry

Year:

2004

Language:

english

File:

PDF, 768 KB

english, 2004

48

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

Zhang, C., Huang, Y., Jiang, Y., Mulpuri, N., Wei, L., Hamelberg, D., Brown, E. M., Yang, J. J.

Journal:

Journal of Biological Chemistry

Year:

2014

Language:

english

File:

PDF, 4.09 MB

english, 2014

49

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

Fajer, Mikolai, Hamelberg, Donald, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 772 KB

english, 2008

50

A dry ligand-binding cavity in a solvated protein

Qvist, J., Davidovic, M., Hamelberg, D., Halle, B.

Journal:

Proceedings of the National Academy of Sciences

Year:

2008

Language:

english

File:

PDF, 489 KB

english, 2008