SMOG@ctbp: simplified deployment of structure-based models in GROMACS

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

Molecular dynamics simulations with coarse-grained 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...

the role of thematic structure in comprehending spoken language

in fact this study is concerned with the relationship between the variation in thematice structure and the comprehension of spoken language. so the study focused on the following questions: 1. is there any relationship between thematic structure and the comprehension of spoken language? 2. which of the themes would have greated thematic force and be easier for the subjects to comprehend? accord...

the effects of changing roughness on the flow structure in the bends

flow in natural river bends is a complex and turbulent phenomenon which affects the scour and sedimentations and causes an irregular bed topography on the bed. for the reason, the flow hydralics and the parameters which affect the flow to be studied and understand. in this study the effect of bed and wall roughness using the software fluent discussed in a sharp 90-degree flume bend with 40.3cm ...

Configuration Based on Simplified Functional Models

How Good Are Simplified Models for Protein Structure Prediction?

Protein structure prediction (PSP) has been one of the most challenging problems in computational biology for several decades. The challenge is largely due to the complexity of the all-atomic details and the unknown nature of the energy function. Researchers have therefore used simplified energy models that consider interaction potentials only between the amino acid monomers in contact on discr...