SMOG@ctbp: simplified deployment of structure-based models in GROMACS.
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A web tool user is able to upload any multi-chain biomolecular system consisting of standard RNA, DNA and amino acids in PDB format and receive as output all files necessary to implement the model in GROMACS.Abstract:
Molecular dynamics simulations with coarsegrained and/or simplified Hamiltonians are an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Structure-based Hamiltonians, simplified models developed from the energy landscape theory of protein folding, have become a standard tool for investigating biomolecular dynamics. SMOG@ctbp is an effort to simplify the use of structure-based models. The purpose of the web server is two fold. First, the web tool simplifies the process of implementing a well-characterized structure-based model on a state-of-the-art, open source, molecular dynamics package, GROMACS. Second, the tutorial-like format helps speed the learning curve of those unfamiliar with molecular dynamics. A web tool user is able to upload any multi-chain biomolecular system consisting of standard RNA, DNA and amino acids in PDB format and receive as output all files necessary to implement the model in GROMACS. Both Ca and all-atom versions of the model are available. SMOG@ctbp resides at http://smog.ucsd.edu.read more
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Conflict of interest statement. None declared.
TL;DR: It is found that women over 50 are more likely to have a family history of diabetes, especially if they are obese, than women under the age of 50.
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Perspective: Coarse-grained models for biomolecular systems.
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How a protein searches for its site on DNA: the mechanism of facilitated diffusion
Leonid A. Mirny,Michael Slutsky,Zeba Wunderlich,Anahita Tafvizi,Jason S. Leith,Andrej Kosmrlj +5 more
TL;DR: It is demonstrated that coupling of DNA recognition with conformational transition within the protein‐DNA complex is essential for fast search and a new mechanism for local distance-dependent search that is likely essential in bacteria is proposed.
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Genomics-aided structure prediction
TL;DR: A theoretical framework that exploits the ever-increasing genomic sequence information for protein structure prediction and incorporates constraints by a large number of non-local contacts estimated from direct coupling analysis (DCA) of co-evolving genomic sequences is introduced.
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Frustration in biomolecules.
TL;DR: Frustration is a fundamental concept in molecular biology as mentioned in this paper, and the energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description.
References
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
TL;DR: A new implementation of the molecular simulation toolkit GROMACS is presented which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines.
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Spin glasses and the statistical mechanics of protein folding
TL;DR: The theory of spin glasses was used to study a simple model of protein folding and the phase diagram was calculated, and the results of dynamics calculations are briefly reported.
Conflict of interest statement. None declared.
TL;DR: It is found that women over 50 are more likely to have a family history of diabetes, especially if they are obese, than women under the age of 50.
Journal ArticleDOI
Theory of protein folding.
José N. Onuchic,Peter G. Wolynes +1 more
TL;DR: This work states that proteins have a rugged funnel-like landscape biased toward the native structure as a result of evolution, and connecting theory and simulations of minimalist models with experiments has completely revolutionized the understanding of the underlying mechanisms that control protein folding.
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Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
TL;DR: In this article, the authors investigated the role of topology in the transition state ensembles of small globular proteins and showed that topology plays a central role in determining the folding mechanism.