期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 11, 期 2, 页码 723-739出版社
AMER CHEMICAL SOC
DOI: 10.1021/ct5007746
关键词
-
资金
- FOCEM (MERCOSUR Structural Convergence Fund) [COF 03/11]
Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and proteinprotein complexes.
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