Developing a fully glycosylated full-length SARS-CoV-2 spike protein model in a viral membrane
This technical study describes all-atom modeling and simulation of a fully glycosylated full-
length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB …
length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB …
GalaxyRefine: Protein structure refinement driven by side-chain repacking
The quality of model structures generated by contemporary protein structure prediction
methods strongly depends on the degree of similarity between the target and available …
methods strongly depends on the degree of similarity between the target and available …
[HTML][HTML] VHH Structural Modelling Approaches: A Critical Review
VHH, ie, VH domains of camelid single-chain antibodies, are very promising therapeutic
agents due to their significant physicochemical advantages compared to classical …
agents due to their significant physicochemical advantages compared to classical …
Homology modeling: an important tool for the drug discovery
TCC França - Journal of Biomolecular Structure and Dynamics, 2015 - Taylor & Francis
In the last decades, homology modeling has become a popular tool to access theoretical
three-dimensional (3D) structures of molecular targets. So far several 3D models of proteins …
three-dimensional (3D) structures of molecular targets. So far several 3D models of proteins …
Structure, dynamics, receptor binding, and antibody binding of the fully glycosylated full-length SARS-CoV-2 spike protein in a viral membrane
The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
mediates host cell entry by binding to angiotensin-converting enzyme 2 (ACE2) and is …
mediates host cell entry by binding to angiotensin-converting enzyme 2 (ACE2) and is …
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 …
Dynamic network modeling of allosteric interactions and communication pathways in the SARS-CoV-2 spike trimer mutants: Differential modulation of conformational …
GM Verkhivker, L Di Paola - The Journal of Physical Chemistry B, 2021 - ACS Publications
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] Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein
The ongoing COVID-19 pandemic caused by the new coronavirus, SARS-CoV-2, calls for
urgent developments of vaccines and antiviral drugs. The spike protein of SARS-CoV-2 (S …
urgent developments of vaccines and antiviral drugs. The spike protein of SARS-CoV-2 (S …
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 …
Structural and dynamical differences in the spike protein RBD in the SARS-CoV-2 variants B. 1.1. 7 and B. 1.351
N Bhattarai, P Baral, BS Gerstman… - The Journal of …, 2021 - ACS Publications
The novel coronavirus (SARS-CoV-2) pandemic that started in late 2019 is responsible for
hundreds of millions of cases worldwide and millions of fatalities. Though vaccines are …
hundreds of millions of cases worldwide and millions of fatalities. Though vaccines are …