SIRAH: A structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics
Darré L, Machado MR, Brandner Giménez A, González HC, Ferreira S, Pantano SF (2015)
Publication Type: Journal article, Original article
Subtype: other
Publication year: 2015
Journal
Book Volume: 11
Pages Range: 723-739-739
Journal Issue: 2
DOI: 10.1021/ct5007746
Abstract
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 protein-protein complexes.
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Uruguay (UY)How to cite
APA:
Darré, L., Machado, M.R., Brandner Giménez, A., González, H.C., Ferreira, S., & Pantano, S.F. (2015). SIRAH: A structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics. Journal of Chemical Theory and Computation, 11(2), 723-739-739. https://dx.doi.org/10.1021/ct5007746
MLA:
Darré, Leonardo, et al. "SIRAH: A structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics." Journal of Chemical Theory and Computation 11.2 (2015): 723-739-739.
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