MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing.

ABSTRACT: Modeling biomolecular assemblies is an important field in computational structural biology. The inherent complexity of their energy landscape and the computational cost associated with modeling large and complex assemblies are major drawbacks for integrative modeling approaches. The so-called coarse-graining approaches, which reduce the degrees of freedom of the system by grouping several atoms into larger "pseudo-atoms," have been shown to alleviate some of those limitations, facilitating the identification of the global energy minima assumed to correspond to the native state of the complex, while making the calculations more efficient. Here, we describe and assess the implementation of the MARTINI force field for DNA into HADDOCK, our integrative modeling platform. We combine it with our

SUBMITTER: Honorato RV 

PROVIDER: S-EPMC6779769 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature