A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states
Solvent accessible surface area (SASA) of proteins has always been considered as a
decisive factor in protein folding and stability studies. It is defined as the surface …
decisive factor in protein folding and stability studies. It is defined as the surface …
CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues
Abstract CHARMM-GUI, http://www. charmm-gui. org, is a web-based graphical user
interface to prepare molecular simulation systems and input files to facilitate the usage of …
interface to prepare molecular simulation systems and input files to facilitate the usage of …
[HTML][HTML] Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces
H Venselaar, TAH Te Beek, RKP Kuipers… - BMC …, 2010 - Springer
Background Many newly detected point mutations are located in protein-coding regions of
the human genome. Knowledge of their effects on the protein's 3D structure provides insight …
the human genome. Knowledge of their effects on the protein's 3D structure provides insight …
A series of PDB-related databanks for everyday needs
WG Touw, C Baakman, J Black… - Nucleic acids …, 2015 - academic.oup.com
We present a series of databanks (http://swift. cmbi. ru. nl/gv/facilities/) that hold information
that is computationally derived from Protein Data Bank (PDB) entries and that might …
that is computationally derived from Protein Data Bank (PDB) entries and that might …
A series of PDB related databases for everyday needs
RP Joosten, TAH Te Beek, E Krieger… - Nucleic acids …, 2010 - academic.oup.com
Abstract The Protein Data Bank (PDB) is the world-wide repository of macromolecular
structure information. We present a series of databases that run parallel to the PDB. Each …
structure information. We present a series of databases that run parallel to the PDB. Each …
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 …
Integrated biophysical modeling of the SARS-CoV-2 spike protein binding and allosteric interactions with antibodies
GM Verkhivker, L Di Paola - The Journal of Physical Chemistry B, 2021 - ACS Publications
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 …
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 …
Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics …
Recent studies have pointed the role of angiotensin-converting enzyme-II (ACE2) in
mediating the entry of SARS-CoV-2 to the host cell by binding to the receptor-binding …
mediating the entry of SARS-CoV-2 to the host cell by binding to the receptor-binding …
[HTML][HTML] Balancing functional tradeoffs between protein stability and ACE2 binding in the SARS-CoV-2 omicron BA. 2, BA. 2.75 and XBB lineages: dynamics-based …
G Verkhivker, M Alshahrani, G Gupta - Viruses, 2023 - mdpi.com
Evolutionary and functional studies suggested that the emergence of the Omicron variants
can be determined by multiple fitness trade-offs including the immune escape, binding …
can be determined by multiple fitness trade-offs including the immune escape, binding …