scholarly journals Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation

2009 ◽  
Vol 11 (12) ◽  
pp. 2077 ◽  
Author(s):  
Alessandra Villa ◽  
Christine Peter ◽  
Nico F. A. van der Vegt
Keyword(s):  
Solvent Free ◽  
Coarse Grained ◽  
Conformational Sampling ◽  
Self Assembling

scholarly journals High-Resolution, Solvent-Free Coarse-Grained Model for Protein-Lipid Interactions

2011 ◽  
Vol 100 (3) ◽  
pp. 640a
Author(s):  
Tristan Bereau ◽  
Zun-Jing Wang ◽  
Markus Deserno
Keyword(s):  
High Resolution ◽  
Solvent Free ◽  
Coarse Grained ◽  
Lipid Interactions ◽  
Coarse Grained Model

scholarly journals Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models

2012 ◽  
Vol 33 (9) ◽  
pp. 937-949 ◽  
Author(s):  
Olga Bezkorovaynaya ◽  
Alexander Lukyanov ◽  
Kurt Kremer ◽  
Christine Peter
Keyword(s):  
Multiscale Simulation ◽  
Coarse Grained ◽  
Conformational Sampling ◽  
Small Peptides

Dissipative Particle Dynamics Studies on the Self-Assembling Dynamics of the Peptide Amphiphiles

2008 ◽  
Vol 1135 ◽  
Author(s):  
Taiga Seki ◽  
Noriyoshi Arai ◽  
Taku Ozawa ◽  
Tomoko Shimada ◽  
Kenji Yasuoka ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
The Self ◽  
Peptide Amphiphiles ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Self Assembling ◽  
Micro Structures ◽  
Good Agreement

ABSTRACTA coarse-grained model of peptide amphiphiles (PA) dissolved in aqueous solution was presented, where the effects of PA concentration, temperature and shear stress upon the self-assembly of PA were numerically studied by dissipative particle dynamics (DPD) simulation. We technically investigate the repulsion parameter aHW which indicates the repulsion force between the hydrophilic head of PA and water molecules, hence, at the same time, indicating the change in temperature. It was found that aHW played an important role in the self-assembly dynamics and in the resulting micro-structures of PA. By imposing shear strain on the simulation system, the formation of wormlike PA micelles was accelerated. The simulation results were in good agreement with our previous experimental results and the mechanism of shear-induced transition was proposed.

scholarly journals An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45

2019 ◽  
Author(s):  
P.I. Koukos ◽  
J. Roel-Touris ◽  
F. Ambrosetti ◽  
C. Geng ◽  
J. Schaarschmidt ◽  
...  
Keyword(s):  
Scoring Function ◽  
Data Driven ◽  
Coarse Grained ◽  
Conformational Sampling ◽  
Model Quality ◽  
Sustained Performance ◽  
Docking Approach ◽  
Binding Pockets ◽  
Integrate Data ◽  
Modelling Process

ABSTRACTOur information-driven docking approach HADDOCK has demonstrated a sustained performance since the start of its participation to CAPRI. This is due, in part, to its ability to integrate data into the modelling process, and to the robustness of its scoring function. We participated in CAPRI both as server and as manual predictors.In CAPRI rounds 38-45, we have used various strategies depending on the information at hand. These ranged from imposing restraints to a few residues identified from literature as being important for the interaction, to binding pockets identified from homologous complexes or template-based refinement / CA-CA restraint-guided docking from identified templates. When relevant, symmetry restraints were used to limit the conformational sampling. We also tested for a large decamer target a new implementation of the MARTINI coarse-grained force field in HADDOCK. Overall in the current rounds, we obtained acceptable or better predictions for 13 and 11 server and manual submissions, respectively, out of the 22 interfaces. Our server performance (acceptable models) was better (59%) than the manual (50%) one, in which we typically experiment with various combinations of protocols and data sources. Again, our simple scoring function based on a linear combination of intermolecular van der Waals and electrostatic energies and an empirical desolvation term demonstrated a good performance in the scoring experiment with a 63% success rate across all 22 interfaces.An analysis of model quality indicates that, while we are consistently performing well in generating acceptable models, there is room for improvement for generating/identifying higher quality models.

Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model

2009 ◽  
Vol 11 (12) ◽  
pp. 2068 ◽  
Author(s):  
Alessandra Villa ◽  
Nico F. A. van der Vegt ◽  
Christine Peter
Keyword(s):  
Degrees Of Freedom ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Self Assembling
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