Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design againstSalmonellaTyphi TolC protein

2017 ◽  
Vol 31 (5) ◽  
pp. e2695 ◽  
Author(s):  
Siew Wen Leong ◽  
Theam Soon Lim ◽  
Asma Ismail ◽  
Yee Siew Choong
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
De Novo ◽  
Dynamics Simulation ◽  
Tolc Protein

scholarly journals De novo protein structure prediction using ultra-fast molecular dynamics simulation

PLoS ONE ◽  
2018 ◽  
Vol 13 (11) ◽  
pp. e0205819 ◽  
Author(s):  
Ngaam J. Cheung ◽  
Wookyung Yu
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulation ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
De Novo ◽  
Dynamics Simulation

scholarly journals Application advances of deep learning methods for de novo drug design and molecular dynamics simulation

2021 ◽  
Author(s):  
Qifeng Bai ◽  
Shuo Liu ◽  
Yanan Tian ◽  
Tingyang Xu ◽  
Antonio Jesús Banegas‐Luna ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Deep Learning ◽  
Molecular Dynamics Simulation ◽  
Drug Design ◽  
De Novo ◽  
Dynamics Simulation ◽  
Learning Methods ◽  
De Novo Drug Design

scholarly journals De novo protein structure prediction using ultra-fast molecular dynamics simulation

2018 ◽  
Author(s):  
Ngaam J. Cheung ◽  
Wookyung Yu
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulation ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
High Efficiency ◽  
Tertiary Structure ◽  
De Novo ◽  
Protein Structures ◽  
Dynamics Simulation

ABSTRACTModern genomics sequencing techniques have provided a massive amount of protein sequences, but experimental endeavor in determining protein structures is largely lagging far behind the vast and unexplored sequences. Apparently, computational biology is playing a more important role in protein structure prediction than ever. Here, we present a system of de novo predictor, termed NiDelta, building on a deep convolutional neural network and statistical potential enabling molecular dynamics simulation for modeling protein tertiary structure. Combining with evolutionary-based residue-contacts, the presented predictor can predict the tertiary structures of a number of target proteins with remarkable accuracy. The proposed approach is demonstrated by calculations on a set of eighteen large proteins from different fold classes. The results show that the ultra-fast molecular dynamics simulation could dramatically reduce the gap between the sequence and its structure at atom level, and it could also present high efficiency in protein structure determination if sparse experimental data is available.

Rotational dynamics and velocity segregation in plastic KCIO4: a molecular dynamics simulation

1998 ◽  
Vol 93 (5) ◽  
pp. 703-711
Author(s):  
F. AFFOUARD ◽  
PH. DEPONDT
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Rotational Dynamics ◽  
Dynamics Simulation

Molecular dynamics simulation of the dynamics of supercooled silica

1998 ◽  
Vol 77 (2) ◽  
pp. 297-303 ◽  
Author(s):  
J. Horbach, W. Kob, K. Binder
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation

Nonequilibrium effects in electron-ion strongly coupled plasmas. Molecular dynamics simulation

2000 ◽  
Vol 10 (PR5) ◽  
pp. Pr5-255-Pr5-258 ◽  
Author(s):  
G. E. Norman ◽  
A. A. Valuev ◽  
I. A. Valuev
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Strongly Coupled ◽  
Strongly Coupled Plasmas ◽  
Nonequilibrium Effects ◽  
Coupled Plasmas
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