scholarly journals FAMSD: A Powerful Protein Modeling Platform that Combines Alignment Methods, Homology Modeling, 3D Structure Quality Estimation and Molecular Dynamics

2009 ◽  
Vol 57 (12) ◽  
pp. 1335-1342 ◽  
Author(s):  
Kazuhiko Kanou ◽  
Mitsuo Iwadate ◽  
Tomoko Hirata ◽  
Genki Terashi ◽  
Hideaki Umeyama ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
3D Structure ◽  
Protein Modeling ◽  
Quality Estimation ◽  
Structure Quality

HOMOLOGY MODELING AND MOLECULAR DYNAMICS STUDY OF HUMAN INOSINE TRIPHOSPHATE PYROPHOSPHATASE

2007 ◽  
Vol 06 (01) ◽  
pp. 141-156
Author(s):  
QING-CHUAN ZHENG ◽  
CHIA-CHUNG SUN
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
Important Determinant ◽  
3D Structure ◽  
Docking Study ◽  
Structure Model ◽  
Flexible Docking ◽  
Inosine Triphosphate Pyrophosphatase ◽  
Modeling Techniques ◽  
Molecular Dynamics Methods

With homology-modeling techniques, molecular mechanics and molecular dynamics methods, a 3D structure model of the human inosine triphosphatase (ITPase; EC 3.6.1.19) is created and refined. This model is further assessed by Profile-3D and ProStat, which confirm that the refined model is reliable. With this model, a flexible docking study is performed, and the results indicate that Arg178, Lys19 and Glu44 are three important determinant residues in substrate binding because they have prominent interaction energies with ITP and form strong hydrogen bonds with ITP. In addition, we further find that the P32T substitution alters the α-helices of ITPase but the β-sheets are almost not changed, and the mutation induces the interaction energy between ITPase and ITP to increase, which are consistent with the conclusion predicted by Sumi et al.8 The results from the mutagenesis imply that Pro32 is vital for the catalytic activity.

scholarly journals Modeling and Molecular Dynamics of the 3D Structure of the HPV16 E7 Protein and Its Variants

2021 ◽  
Vol 22 (3) ◽  
pp. 1400
Author(s):  
Ciresthel Bello-Rios ◽  
Sarita Montaño ◽  
Olga Lilia Garibay-Cerdenares ◽  
Lilian Esmeralda Araujo-Arcos ◽  
Marco Antonio Leyva-Vázquez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Epidemiological Studies ◽  
Dynamics Simulation ◽  
Structural Refinement ◽  
Oncogenic Potential ◽  
Structural Differences ◽  
Reference Protein ◽  
E6 And E7 ◽  
First Time

The oncogenic potential of high-risk human papillomavirus (HPV) is predicated on the production of the E6 and E7 oncoproteins, which are responsible for disrupting the control of the cell cycle. Epidemiological studies have proposed that the presence of the N29S and H51N variants of the HPV16 E7 protein is significantly associated with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains uncertain. An analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose, for the first time, a 3D structure of the E7 reference protein and two of Its variants (N29S and H51N), and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.

A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling, docking, de novo drug design and molecular dynamics analysis

2009 ◽  
Vol 14 (2) ◽  
pp. 257-276 ◽  
Author(s):  
Serdar Durdagi ◽  
Manthos G. Papadopoulos ◽  
Panagiotis G. Zoumpoulakis ◽  
Catherine Koukoulitsa ◽  
Thomas Mavromoustakos
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Homology Modeling ◽  
Cannabinoid Receptors ◽  
De Novo ◽  
Computational Study ◽  
Dynamics Analysis ◽  
De Novo Drug Design

Combining fragment homology modeling with molecular dynamics aims at prediction of Ca2+ binding sites in CaBPs

2013 ◽  
Vol 27 (8) ◽  
pp. 697-705 ◽  
Author(s):  
ChunLi Pang ◽  
TianGuang Cao ◽  
JunWei Li ◽  
MengWen Jia ◽  
SuHua Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
Binding Sites
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