Ribosome Builder: A software project to simulate the ribosome

Knight, William A.; Hill, Walter E.; Lodmell, J. Stephen

doi:10.1016/j.compbiolchem.2005.01.001

Cited by 7 publications

(4 citation statements)

References 133 publications

(147 reference statements)

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“…64 We chose an extended starting configuration as this structure is a simple starting point, with maximal radius of gyration and root mean square deviation from the native structure. We note that the choice of the starting configuration can affect the folding pathway 36 and our approach is different from approaches where thermally unfolded configurations were taken as starting conformation.…”

Section: Simulation Details and Analysismentioning

confidence: 99%

A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides

Peter

Pivkin

Shea

2015

The Journal of Chemical Physics

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In Monte-Carlo simulations of protein folding, pathways and folding times depend on the appropriate choice of the Monte-Carlo move or process path. We developed a generalized set of process paths for a hybrid kinetic Monte Carlo-Molecular dynamics algorithm, which makes use of a novel constant time-update and allows formation of α-helical and β-stranded secondary structures. We apply our new algorithm to the folding of 3 different proteins: TrpCage, GB1, and TrpZip4. All three systems are seen to fold within the range of the experimental folding times. For the β-hairpins, we observe that loop formation is the rate-determining process followed by collapse and formation of the native core. Cluster analysis of both peptides reveals that GB1 folds with equal likelihood along a zipper or a hydrophobic collapse mechanism, while TrpZip4 follows primarily a zipper pathway. The difference observed in the folding behavior of the two proteins can be attributed to the different arrangements of their hydrophobic core, strongly packed, and dry in case of TrpZip4, and partially hydrated in the case of GB1.

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Section: Simulation Details and Analysismentioning

confidence: 99%

A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides

Peter

Pivkin

Shea

2015

The Journal of Chemical Physics

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“…All extended polypeptide conformations were built using the Ribosome program. 49 For the simulation of the GB1 peptide, we centered the extended protein in a box with dimensions 7.3 Â 7.3 Â 7.3 nm 3 and added 12672 SPC/E waters. We used the SPC/E model, which has self-diffusion coefficients comparable to the experiment.…”

Section: Simulation Parameters and System Preparationmentioning

confidence: 99%

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

Peter

Shea

Pivkin

2016

Phys. Chem. Chem. Phys.

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In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC). The new development significantly can reduce the amount of replicas and the computational cost needed to enhance sampling in protein simulations. We introduce 2 different methods which primarily differ in the exchange scheme between the parallel ensembles. We apply this approach on folding of 2 different β-stranded peptides: the C-terminal β-hairpin fragment of GB1 and TrpZip4. Additionally, we use the new simulation technique to study the folding of TrpCage, a small fast folding α-helical peptide. Subsequently, we apply the new methodology on conformation changes in signaling of the light-oxygen voltage (LOV) sensitive domain from Avena sativa (AsLOV2). Our results agree well with data reported in the literature. In simulations of dialanine, we compare the statistical sampling of the 2 techniques with conventional REMD and analyze their performance. The new techniques can reduce the computational cost of REMD significantly and can be used in enhanced sampling simulations of biomolecules.

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“…RNA-RNA and protein-RNA interactions were determined using the 16S secondary structure 31 and PDB 2AW7 9 and 2J00 10 in conjunction with RiboBuilder software 42 and PyMOL.…”

Section: Structural Analysismentioning

confidence: 99%

The Genesis of Ribosome Structure: How a Protein Generates RNA Structure in Real Time

Woolstenhulme

Hill

2009

Journal of Molecular Biology

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Ribosome Builder: A software project to simulate the ribosome

Cited by 7 publications

References 133 publications

A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides

A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

The Genesis of Ribosome Structure: How a Protein Generates RNA Structure in Real Time

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