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The SARS-CoV-2 Spike variant D614G favors an open conformational state
The COVID-19 global pandemic is an international health emergency. It is caused by the
SARS-CoV-2 virus, which binds with its trimeric Spike protein to the ACE2 receptor in the …
SARS-CoV-2 virus, which binds with its trimeric Spike protein to the ACE2 receptor in the …
Comparative perturbation-based modeling of the SARS-CoV-2 spike protein binding with host receptor and neutralizing antibodies: Structurally adaptable allosteric …
GM Verkhivker, S Agajanian, DY Oztas, G Gupta - Biochemistry, 2021 - ACS Publications
In this study, we used an integrative computational approach to examine molecular
mechanisms and determine functional signatures underlying the role of functional residues …
mechanisms and determine functional signatures underlying the role of functional residues …
Molecular insights into the misfolding and dimerization dynamics of the full-length α-synuclein from atomistic discrete molecular dynamics simulations
The misfolding and pathological aggregation of α-synuclein forming insoluble amyloid
deposits is associated with Parkinson's disease, the second most common …
deposits is associated with Parkinson's disease, the second most common …
Integrated biophysical modeling of the SARS-CoV-2 spike protein binding and allosteric interactions with antibodies
Structural and biochemical studies of the severe acute respiratory syndrome (SARS)-CoV-2
spike glycoproteins and complexes with highly potent antibodies have revealed multiple …
spike glycoproteins and complexes with highly potent antibodies have revealed multiple …
Dynamic network modeling of allosteric interactions and communication pathways in the SARS-CoV-2 spike trimer mutants: Differential modulation of conformational …
The rapidly growing body of structural and biochemical studies of the SARS-CoV-2 spike
glycoprotein has revealed a variety of distinct functional states with radically different …
glycoprotein has revealed a variety of distinct functional states with radically different …
[HTML][HTML] Efficient preparation and analysis of membrane and membrane protein systems
Molecular dynamics (MD) simulations have become a highly important technique to
consider lipid membrane systems, and quite often they provide considerable added value to …
consider lipid membrane systems, and quite often they provide considerable added value to …
Dynamic profiling of binding and allosteric propensities of the SARS-CoV-2 spike protein with different classes of antibodies: mutational and perturbation-based …
G Verkhivker, S Agajanian, D Oztas… - Journal of chemical …, 2021 - ACS Publications
The functional adaptability and conformational plasticity of SARS-CoV-2 spike proteins allow
for the efficient modulation of complex phenotypic responses to the host receptor and …
for the efficient modulation of complex phenotypic responses to the host receptor and …
Substitution of PINK1 Gly411 modulates substrate receptivity and turnover
The ubiquitin (Ub) kinase-ligase pair PINK1-PRKN mediates the degradation of damaged
mitochondria by macroautophagy/autophagy (mitophagy). PINK1 surveils mitochondria and …
mitochondria by macroautophagy/autophagy (mitophagy). PINK1 surveils mitochondria and …
Integrin activation by the lipid molecule 25-hydroxycholesterol induces a proinflammatory response
Integrins are components of cell-matrix adhesions, and function as scaffolds for various
signal transduction pathways. So far no lipid ligand for integrin has been reported. Here we …
signal transduction pathways. So far no lipid ligand for integrin has been reported. Here we …
Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations
TD Romo, N Leioatts… - Journal of computational …, 2014 - Wiley Online Library
LOOS (Lightweight Object Oriented Structure‐analysis) is a C++ library designed to facilitate
making novel tools for analyzing molecular dynamics simulations by abstracting out the …
making novel tools for analyzing molecular dynamics simulations by abstracting out the …