Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants
Despite an unprecedented global gain in knowledge since the emergence of SARS-CoV-2,
almost all mechanistic knowledge related to the molecular and cellular details of viral …
almost all mechanistic knowledge related to the molecular and cellular details of viral …
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 …
An overview of several inhibitors for Alzheimer's disease: characterization and failure
Amyloid beta (Aβ) oligomers are the most neurotoxic aggregates causing neuronal death
and cognitive damage. A detailed elucidation of the aggregation pathways from oligomers to …
and cognitive damage. A detailed elucidation of the aggregation pathways from oligomers to …
Characterization of structural and energetic differences between conformations of the SARS-CoV-2 spike protein
The novel coronavirus disease 2019 (COVID-19) pandemic has disrupted modern societies
and their economies. The resurgence in COVID-19 cases as part of the second wave is …
and their economies. The resurgence in COVID-19 cases as part of the second wave is …
Quantitative determination of mechanical stability in the novel coronavirus spike protein
We report on the novel observation about the gain in nanomechanical stability of the SARS-
CoV-2 (CoV2) spike (S) protein in comparison with SARS-CoV from 2002 (CoV1). Our …
CoV-2 (CoV2) spike (S) protein in comparison with SARS-CoV from 2002 (CoV1). Our …
Mapping mechanostable pulling geometries of a therapeutic anticalin/CTLA-4 protein complex
We used single-molecule AFM force spectroscopy (AFM-SMFS) in combination with click
chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from …
chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from …
Protein energy landscape exploration with structure-based models
S Neelamraju, DJ Wales, S Gosavi - Current opinion in structural biology, 2020 - Elsevier
Exploring the multi-dimensional energy landscape of a large protein in detail is a
computational challenge. Such investigations may include analysis of multiple folding …
computational challenge. Such investigations may include analysis of multiple folding …
Treatment of flexibility of protein backbone in simulations of protein–ligand interactions using steered molecular dynamics
To ensure that an external force can break the interaction between a protein and a ligand,
the steered molecular dynamics simulation requires a harmonic restrained potential applied …
the steered molecular dynamics simulation requires a harmonic restrained potential applied …
Nanomechanical footprint of SARS-CoV-2 variants in complex with a potent nanobody by molecular simulations
LF Cofas-Vargas, GE Olivos-Ramirez, M Chwastyk… - Nanoscale, 2024 - pubs.rsc.org
Rational design of novel antibody therapeutics against viral infections such as coronavirus
relies on surface complementarity and high affinity for their effectiveness. Here, we explore …
relies on surface complementarity and high affinity for their effectiveness. Here, we explore …
Determination of contact maps in proteins: A combination of structural and chemical approaches
K Wołek, À Gómez-Sicilia, M Cieplak - The Journal of chemical physics, 2015 - pubs.aip.org
Contact map selection is a crucial step in structure-based molecular dynamics modelling of
proteins. The map can be determined in many different ways. We focus on the methods in …
proteins. The map can be determined in many different ways. We focus on the methods in …