Nested Sampling for a Coarse-Grained Protein Model 34
Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data
... ribbon model: the conformation reported in the PDB, in green, and the conformation generated by SIMS which provides estimates of protection factors that best fit the experimental HDX data, in ...
14
Coarse-grained model of entropic allostery
... quantitative, coarse-grained model of entropic allostery, which suggests design rules for internal cohesive potentials in proteins employing this ...the protein. The model may be ...
5
Graphics Processing Unit Accelerated Coarse-Grained Protein-Protein Docking
... Thread blocks and grids implicitly loop over all elements in a data set: serially, a 1D thread block would be a simple loop, a 2D thread block would be a nested loop etc. Within a thread block, threads can ...
230
Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective
... Understanding protein-protein association is crucial in revealing the molecular basis of many biological pro- ...study protein-protein association from an energy landscape ...a ...
9
Graphics processing unit accelerated coarse-grained protein-protein docking
... the host and the device have separate memory, referred to as host memory and device memory, respectively. Thread blocks and grids implicitly loop over all elements in a data set: serially, a 1D thread block would be a ...
229
Exploring Protein–Nanoparticle Interactions with Coarse‐Grained Protein Folding Models
... quantitative model to explore protein structure, energetics, and function on spherical NPs, as it captures both the surface curvature of the NP and the surface chemistry that influences pro- tein–NP ...
10
Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics
... normal model analysis based on a C a C a quasiharmonic potential (22) provides a reasonable description of the equilibrium defor- mability pattern predicted by atomistic MD ...same coarse-grained ...
12
Coarse-grained Simulation of Azurin Crystal Complex System: Protein–protein Interactions
... of protein function analyses focus mainly on the physical properties of a sin- gle ...the protein–protein interactions for gaining insights into molecular crowding effects on protein ...
8
On coarse-grained Normal Mode Analysis and refined Gaussian Network Model for protein structure fluctuations
... Therefore an alternative method is needed that does not depend on MD simulations. In Normal Mode Analysis, a complete analytical solution of the system of equations of motion can be derived with an assumption that the ...
80
Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model
... simplified model combined with a fast dynamics algorithm gives us the opportunity to study the folding process for many successful folding events starting from the extended ...the protein is mainly present ...
9
Addition of flexible linkers to GPU-accelerated coarse-grained simulations of protein-protein docking
... this model thus reduces the number of bodies in the simulation by a factor of approximately ...a protein are treated as rigid bodies, which may be connected by flexible linkers modelled as ...
88
High Performance Computing with Coarse Grained Model of Biological Macromolecules
... other coarse-grained force fields, UCGM is a physics-based force field, indepen- dent of structural databases and applicable to treat non-standard ...levels: coarse-grained and ...
13
Testing the transferability of a coarse grained model to intrinsically disordered proteins
... PLUM model, introduced by Bereau and Deserno, 27 is designed to model protein folding and ...the protein structure is ‘‘not known, not well defined, strongly perturbed from the native state, ...
10
Coarse-Grained Simulation Approaches for Protein Integration and Translocation via the Sec Translocon
... a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translo- cation and membrane integration via the Sec translocon, while retaining ...
135
Thermodynamics of ice interfaces and structures within a coarse grained model of water
... At the beginning of the simulation, the initial state is prepared according to a set of defined conditions. The system can be initialised in a well defined ordered state, such as a solid crystal lattice with all ...
185
Modeling RNA, protein, and synthetic molecules using coarse-grained and all-atom representations
... of the potential energy function nor do they allow for sufficient sampling of binding conformations. QM calculations of binding free energy 143-145 are limited to small, predetermined binding sites. Bridging the ...
136
Systematic derivation of hybrid coarse grained models
... toy model for a binary alloy. The system is coarse-grained by combining single repeating units into ...and coarse-grained dynamics in the model described and, more importantly, ...
32
A coarse grained transport model for nanofluidic systems
... the model can be improved by changing the potential form and ther- mostat ...the model was to simulate transport at high shear rates where the molecular dynamics simulations start to deviate from linear ...
56
A Structurally Relevant Coarse-Grained Model for Cholesterol
... CHOL model was optimized that is capable of predicting the structural properties of atomistic CHOL as seen by the agreement ob- tained in the RDFs, the crystal parameters, and configuration snapshots comparing the ...
10
Simplified Coarse Grained Dynamic Model for Real Gases
... simplified model is proposed for an easy understanding of the coarse- grained technique and for achieving a first approximation to the behavior of ...proposed model, on Carbon Dioxide, are ...
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