cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA
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It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein-DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive ...
Sequence dependent mechanics of DNA is believed to play a central role in the functioning of the cell through the expression of genetic information. Nucleosome positioning, gene regulation, DNA looping and packaging within the cell are only some of the pro ...
We present a molecular dynamics study on the interaction of styryl-type voltage-sensitive dyes with a lipid membrane. In this work, voltage-sensitive dyes are proposed as interesting model amphiphiles for biomolecular simulation, due to the wealth of bioph ...
Proteins have the ability to assemble in multimeric states to perform their specific biological function. Unfortunately, characterizing experimentally these structures at atomistic resolution is usually difficult. For this reason, in silico methodologies a ...
DNA damages induced by oxidative intrastrand cross-links have been the subject of intense research during the past decade. Yet, the currently available experimental protocols used to isolate such lesions only allow to get structural information about linke ...
Molecular dynamics (MD) simulations have increasingly contributed to the understanding of biomolecular processes, allowing for predictions of thermodynamic and structural properties. Unfortunately, the holy grail of protein structure prediction was soon fo ...
Proteins have a complex free-energy landscape because of their rich topol. and the nature of their nonbonded interaction potential. This has important consequences because the roughness of the landscape affects the ease with which a chain folds and also de ...
Microorganisms provide a wealth of bio-degradative potential in the reduction and elimination of xenobiotic compounds in the environment. One useful metric to evaluate potential biodegradation pathways is thermodynamic feasibility. However, experimental da ...
We derived an orbital dependent Kohn-Sham based scheme for the correction of the self-interaction error in DFT, which is particularly suited for the study of open shell molecular systems. Our approach is based on a weighted form of the Perdew and Zunger (P ...
The novel fast-growth or multiple steering mol. dynamics (MSMD) technique has been recently developed by Jarzynski to calc. free energy profiles along general transformation pathways (Phys. Rev. Lett. 1997, 78, 2690-2693; Phys. Rev. E 1997, 56, 5018-5035). ...
