Astrid Brandner - Academia.edu (original) (raw)
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Papers by Astrid Brandner
Journal of Chemical Theory and Computation, 2015
Modeling of macromolecular structures and interactions represents an important challenge for comp... more 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. a N indicates the number of residues. Values reported correspond to the average calculated over the last 100 ns of each μs. Parentheses and square brackets indicate standard deviations and values calculated from the experimental structure, respectively.
Lecture Notes in Computer Science, 2013
ABSTRACT We present a comparison between atomistic and coarse grain models for DNA developed in o... more ABSTRACT We present a comparison between atomistic and coarse grain models for DNA developed in our group, which we introduce here with the name SIRAH. Molecular dynamics of DNA fragments performed using implicit and explicit solvation approaches show good agreement in structural and dynamical features with published state of the art atomistic simulations of double stranded DNA (using Amber and Charmm force fields). The study of the multi-microsecond timescale results in counterion condensation on DNA, in coincidence with high-resolution X-ray crystals. This result indicates that our model for solvation is able to correctly reproduce ionic strength effects, which are very difficult to capture by CG schemes.
Journal of Chemical Theory and Computation, 2015
Modeling of macromolecular structures and interactions represents an important challenge for comp... more 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. a N indicates the number of residues. Values reported correspond to the average calculated over the last 100 ns of each μs. Parentheses and square brackets indicate standard deviations and values calculated from the experimental structure, respectively.
Lecture Notes in Computer Science, 2013
ABSTRACT We present a comparison between atomistic and coarse grain models for DNA developed in o... more ABSTRACT We present a comparison between atomistic and coarse grain models for DNA developed in our group, which we introduce here with the name SIRAH. Molecular dynamics of DNA fragments performed using implicit and explicit solvation approaches show good agreement in structural and dynamical features with published state of the art atomistic simulations of double stranded DNA (using Amber and Charmm force fields). The study of the multi-microsecond timescale results in counterion condensation on DNA, in coincidence with high-resolution X-ray crystals. This result indicates that our model for solvation is able to correctly reproduce ionic strength effects, which are very difficult to capture by CG schemes.