Multifaceted computational modeling in glycoscience
S Perez, O Makshakova - Chemical Reviews, 2022 - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …
Recent advances in coarse-grained models for biomolecules and their applications
N Singh, W Li - International journal of molecular sciences, 2019 - mdpi.com
Molecular dynamics simulations have emerged as a powerful tool to study biological
systems at varied length and timescales. The conventional all-atom molecular dynamics …
systems at varied length and timescales. The conventional all-atom molecular dynamics …
Combining the MARTINI and structure-based coarse-grained approaches for the molecular dynamics studies of conformational transitions in proteins
The application of coarse-grained (CG) models in biology is essential to access large length
and time scales required for the description of many biological processes. The ELNEDIN …
and time scales required for the description of many biological processes. The ELNEDIN …
Optimizing Gō-MARTINI coarse-grained model for F-BAR protein on lipid membrane
Coarse-grained (CG) molecular dynamics (MD) simulations allow us to access much larger
length and time scales than atomistic MD simulations, providing an attractive alternative to …
length and time scales than atomistic MD simulations, providing an attractive alternative to …
Extending the Martini Coarse-Grained Force Field to N-Glycans
Glycans play a vital role in a large number of cellular processes. Their complex and flexible
nature hampers structure–function studies using experimental techniques. Molecular …
nature hampers structure–function studies using experimental techniques. Molecular …
A novel supra coarse-grained model for cellulose
Cellulose being the most widely available biopolymer on Earth is attracting significant
interest from the industry and research communities. While molecular simulations can be …
interest from the industry and research communities. While molecular simulations can be …
Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: Fixed contacts, switchable contacts and those described by …
Ł Mioduszewski, J Bednarz, M Chwastyk… - Computer Physics …, 2023 - Elsevier
We present a coarse-grained C α-based protein model that can be used to simulate
structured, intrinsically disordered and partially disordered proteins. We use a Go-like …
structured, intrinsically disordered and partially disordered proteins. We use a Go-like …
[HTML][HTML] Mechanical and thermodynamic properties of Aβ42, Aβ40, and α-synuclein fibrils: a coarse-grained method to complement experimental studies
We perform molecular dynamics simulation on several relevant biological fibrils associated
with neurodegenerative diseases such as Aβ 40, Aβ 42, and α-synuclein systems to obtain a …
with neurodegenerative diseases such as Aβ 40, Aβ 42, and α-synuclein systems to obtain a …
Differentiating between inactive and active states of rhodopsin by atomic force microscopy in native membranes
Membrane proteins, including G protein-coupled receptors (GPCRs), present a challenge in
studying their structural properties under physiological conditions. Moreover, to better …
studying their structural properties under physiological conditions. Moreover, to better …
Nanomechanical stability of Aβ tetramers and fibril-like structures: molecular dynamics simulations
Alzheimer's disease (AD) is a neurodegenerative disorder and one of the main causes of
dementia. The disease is associated with amyloid beta (Aβ) peptide aggregation forming …
dementia. The disease is associated with amyloid beta (Aβ) peptide aggregation forming …