Ab Initio and Hybrid Molecular Dynamics Simulations of the Active Site of Human Carbonic Anhydrase II: A Test Case Study

ACS Symposium Series - Combined Quantum Mechanical and Molecular Mechanical Methods ◽

10.1021/bk-1998-0712.ch017 ◽

1998 ◽

pp. 264-274 ◽

Author(s):

Ursula Röthlisberger

Keyword(s):

Molecular Dynamics ◽

Carbonic Anhydrase ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Active Site ◽

Carbonic Anhydrase Ii ◽

Test Case ◽

Human Carbonic Anhydrase ◽

Dynamics Simulations

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Molecular Dynamics Simulations of H2NSO2C6H4CONH(Gly)3OBn Bound to the Active Site of Human Carbonic Anhydrase II

Journal of the American Chemical Society ◽

10.1021/ja00128a001 ◽

1995 ◽

Vol 117 (23) ◽

pp. 6153-6164 ◽

Author(s):

Donovan N. Chin ◽

George M. Whitesides

Keyword(s):

Molecular Dynamics ◽

Carbonic Anhydrase ◽

Molecular Dynamics Simulations ◽

Active Site ◽

Carbonic Anhydrase Ii ◽

Human Carbonic Anhydrase ◽

Dynamics Simulations

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Dynamic Force Field Models: Molecular Dynamics Simulations of Human Carbonic Anhydrase II Using a Quantum Mechanical/Molecular Mechanical Coupled Potential

The Journal of Physical Chemistry ◽

10.1021/j100028a030 ◽

1995 ◽

Vol 99 (28) ◽

pp. 11266-11275 ◽

Author(s):

David S. Hartsough ◽

Kenneth M. Jr. Merz

Keyword(s):

Molecular Dynamics ◽

Carbonic Anhydrase ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Carbonic Anhydrase Ii ◽

Quantum Mechanical ◽

Dynamic Force ◽

Human Carbonic Anhydrase ◽

Dynamics Simulations

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Molecular dynamics simulations of human carbonic anhydrase II: Insight into experimental results and the role of solvation

Proteins Structure Function and Bioinformatics ◽

10.1002/(sici)1097-0134(19981001)33:1<119::aid-prot11>3.0.co;2-o ◽

1998 ◽

Vol 33 (1) ◽

pp. 119-134 ◽

Author(s):

Dongsheng Lu ◽

Gregory A. Voth

Keyword(s):

Molecular Dynamics ◽

Carbonic Anhydrase ◽

Molecular Dynamics Simulations ◽

Experimental Results ◽

Carbonic Anhydrase Ii ◽

Human Carbonic Anhydrase ◽

Dynamics Simulations ◽

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Identification of potent human carbonic anhydrase IX inhibitors: a combination of pharmacophore modeling, 3D-QSAR, virtual screening and molecular dynamics simulations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2020.1860132 ◽

2020 ◽

pp. 1-16

Author(s):

Varun Chahal ◽

Sonam Nirwan ◽

Mallika Pathak ◽

Rita Kakkar

Keyword(s):

Molecular Dynamics ◽

Virtual Screening ◽

Carbonic Anhydrase ◽

Molecular Dynamics Simulations ◽

3D Qsar ◽

Pharmacophore Modeling ◽

Carbonic Anhydrase Ix ◽

Human Carbonic Anhydrase ◽

Dynamics Simulations

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Stabilization of antibody structure upon association to a human carbonic anhydrase IX epitope studied by X-ray crystallography, microcalorimetry, and molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21821 ◽

2007 ◽

Vol 71 (3) ◽

pp. 1275-1287 ◽

Author(s):

Vlastimil Král ◽

Pavel Mader ◽

Renata Collard ◽

Milan Fábry ◽

Magdaléna Hořejší ◽

...

Keyword(s):

Molecular Dynamics ◽

Carbonic Anhydrase ◽

Molecular Dynamics Simulations ◽

Carbonic Anhydrase Ix ◽

X Ray ◽

X Ray Crystallography ◽

Antibody Structure ◽

Human Carbonic Anhydrase ◽

Dynamics Simulations

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Energy loss and surface temperature effects in ab initio molecular dynamics simulations: N adsorption on Ag(111) as a case study

Physical Review B ◽

10.1103/physrevb.96.085437 ◽

2017 ◽

Vol 96 (8) ◽

Author(s):

Dino Novko ◽

Ivor Lončarić ◽

María Blanco-Rey ◽

J. Iñaki Juaristi ◽

Maite Alducin

Keyword(s):

Molecular Dynamics ◽

Energy Loss ◽

Surface Temperature ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Temperature Effects ◽

Ab Initio Molecular Dynamics ◽

Dynamics Simulations

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Binding of substrate CO2 to the active site of human carbonic anhydrase II: A molecular dynamics study

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.87.16.6475a ◽

1990 ◽

Vol 87 (16) ◽

pp. 6475-6475

Keyword(s):

Molecular Dynamics ◽

Carbonic Anhydrase ◽

Active Site ◽

Carbonic Anhydrase Ii ◽

Human Carbonic Anhydrase

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Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Carbonic Anhydrase II Apo-Enzyme

ACS Omega ◽

10.1021/acsomega.7b01414 ◽

2017 ◽

Vol 2 (11) ◽

pp. 8414-8420 ◽

Author(s):

Huishu Ma ◽

Anbang Li ◽

Kaifu Gao

Keyword(s):

Molecular Dynamics ◽

Carbonic Anhydrase ◽

Molecular Dynamics Simulations ◽

Conformational Transitions ◽

Carbonic Anhydrase Ii ◽

Dynamics Simulations

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Active Site Cysteine Is Protonated in the PAD4 Michaelis Complex: Evidence from Born−Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/jp903173c ◽

2009 ◽

Vol 113 (38) ◽

pp. 12750-12758 ◽

Author(s):

Zhihong Ke ◽

Yanzi Zhou ◽

Po Hu ◽

Shenglong Wang ◽

Daiqian Xie ◽

...

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Active Site ◽

Active Site Cysteine ◽

Dynamics Simulations

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Binding of substrate CO2 to the active site of human carbonic anhydrase II: a molecular dynamics study.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.87.10.3675 ◽

1990 ◽

Vol 87 (10) ◽

pp. 3675-3679 ◽

Author(s):

J. Y. Liang ◽

W. N. Lipscomb

Keyword(s):

Molecular Dynamics ◽

Carbonic Anhydrase ◽

Active Site ◽

Carbonic Anhydrase Ii ◽

Human Carbonic Anhydrase

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