Ligand Binding Site Identification by Higher Dimension Molecular Dynamics

Journal of Chemical Information and Modeling ◽

10.1021/ci300561b ◽

2013 ◽

Vol 53 (3) ◽

pp. 674-680 ◽

Author(s):

Achani K. Yatawara ◽

Milan Hodoscek ◽

Dale F. Mierke

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Binding Site ◽

Higher Dimension ◽

Ligand Binding Site ◽

Binding Site Identification ◽

Site Identification

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Computational allosteric ligand binding site identification on Ras proteins

Acta Biochimica et Biophysica Sinica ◽

10.1093/abbs/gmv100 ◽

2015 ◽

pp. gmv100 ◽

Author(s):

Michael McCarthy ◽

Priyanka Prakash ◽

Alemayehu A. Gorfe

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Ligand Binding Site ◽

Ras Proteins ◽

Binding Site Identification ◽

Site Identification

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pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins

PLoS Computational Biology ◽

10.1371/journal.pcbi.1004469 ◽

2015 ◽

Vol 11 (10) ◽

pp. e1004469 ◽

Author(s):

Priyanka Prakash ◽

Abdallah Sayyed-Ahmad ◽

Alemayehu A. Gorfe

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Ligand Binding Site ◽

Binding Site Identification ◽

Membrane Bound ◽

Site Identification

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SITEHOUND-web: a server for ligand binding site identification in protein structures

Nucleic Acids Research ◽

10.1093/nar/gkp281 ◽

2009 ◽

Vol 37 (Web Server) ◽

pp. W413-W416 ◽

Author(s):

M. Hernandez ◽

D. Ghersi ◽

R. Sanchez

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Protein Structures ◽

Ligand Binding Site ◽

Binding Site Identification ◽

Site Identification

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Ligand Binding Site Identification in Membrane-Bound Oncogenic K-Ras

Biophysical Journal ◽

10.1016/j.bpj.2013.11.3667 ◽

2014 ◽

Vol 106 (2) ◽

pp. 662a

Author(s):

Priyanka Prakash ◽

Alemayehu A. Gorfe

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Ligand Binding Site ◽

Binding Site Identification ◽

Membrane Bound ◽

Site Identification

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Mixed-Probe Simulation and Probe-Derived Surface Topography Map Analysis for Ligand Binding Site Identification

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.7b00130 ◽

2017 ◽

Vol 13 (4) ◽

pp. 1851-1861 ◽

Author(s):

Abdallah Sayyed-Ahmad ◽

Alemayehu A. Gorfe

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Surface Topography ◽

Ligand Binding Site ◽

Binding Site Identification ◽

Map Analysis ◽

Site Identification

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Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.9b00751 ◽

2019 ◽

Vol 15 (11) ◽

pp. 6524-6535 ◽

Author(s):

Hugo Guterres ◽

Hui Sun Lee ◽

Wonpil Im

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Binding Site ◽

Structure Refinement ◽

Ligand Binding Site ◽

Site Structure ◽

Predicted Binding Site

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Negative allosteric modulators of cannabinoid receptor 2: protein modeling, binding site identification and molecular dynamics simulations in the presence of an orthosteric agonist

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1567384 ◽

2019 ◽

Vol 38 (1) ◽

pp. 32-47 ◽

Author(s):

Pankaj Pandey ◽

Kuldeep K. Roy ◽

Robert J. Doerksen

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Binding Site ◽

Cannabinoid Receptor ◽

Protein Modeling ◽

Allosteric Modulators ◽

Cannabinoid Receptor 2 ◽

Binding Site Identification ◽

Dynamics Simulations ◽

Site Identification

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Binding site identification and role of permanent water molecule of PIM-3 kinase: A molecular dynamics study

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2015.07.004 ◽

2015 ◽

Vol 62 ◽

pp. 276-282 ◽

Author(s):

Zaheer Ul-Haq ◽

Sana Gul ◽

Saman Usmani ◽

Abdul Wadood ◽

Waqasuddin Khan

Keyword(s):

Molecular Dynamics ◽

Water Molecule ◽

Binding Site ◽

Binding Site Identification ◽

Site Identification ◽

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Possible allosteric binding site on Gyrase B, a key target for novel anti-TB drugs: homology modelling and binding site identification using molecular dynamics simulation and binding free energy calculations

Medicinal Chemistry Research ◽

10.1007/s00044-014-1279-3 ◽

2014 ◽

Vol 24 (5) ◽

pp. 2055-2074 ◽

Author(s):

Sarentha Chetty ◽

Mahmoud E. S. Soliman

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Site ◽

Binding Free Energy ◽

Homology Modelling ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Binding Site Identification ◽

Binding Free Energy Calculations ◽

Site Identification

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Constraints of Opsin Structure on the Ligand-binding Site: Studies with Ring-fused Retinals¶

Photochemistry and Photobiology ◽

10.1562/0031-8655(2002)076<0606:coosot>2.0.co;2 ◽

2002 ◽

Vol 76 (6) ◽

pp. 606 ◽

Author(s):

Takahiro Hirano ◽

In Taek Lim ◽

Don Moon Kim ◽

Xiang-Guo Zheng ◽

Kazuo Yoshihara ◽

...

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Ligand Binding Site

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