Dielectric continuum methods for quantum chemistry
JM Herbert - Wiley Interdisciplinary Reviews: Computational …, 2021 - Wiley Online Library
This review describes the theory and implementation of implicit solvation models based on
continuum electrostatics. Within quantum chemistry this formalism is sometimes …
continuum electrostatics. Within quantum chemistry this formalism is sometimes …
gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS
MS Valdés-Tresanco… - Journal of chemical …, 2021 - ACS Publications
Molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area is one of the
most popular methods to estimate binding free energies. This method has been proven to …
most popular methods to estimate binding free energies. This method has been proven to …
Boosting the full potential of PyMOL with structural biology plugins
Over the past few decades, the number of available structural bioinformatics pipelines,
libraries, plugins, web resources and software has increased exponentially and become …
libraries, plugins, web resources and software has increased exponentially and become …
De novo design of protein interactions with learned surface fingerprints
Physical interactions between proteins are essential for most biological processes
governing life. However, the molecular determinants of such interactions have been …
governing life. However, the molecular determinants of such interactions have been …
The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein
The multifunctional nucleocapsid (N) protein in SARS-CoV-2 binds the~ 30 kb viral RNA
genome to aid its packaging into the 80–90 nm membrane-enveloped virion. The N protein …
genome to aid its packaging into the 80–90 nm membrane-enveloped virion. The N protein …
Omicron (BA. 1) and sub‐variants (BA. 1.1, BA. 2, and BA. 3) of SARS‐CoV‐2 spike infectivity and pathogenicity: A comparative sequence and structural‐based …
The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2)
has now spread throughout the world. We used computational tools to assess the spike …
has now spread throughout the world. We used computational tools to assess the spike …
Mutations on RBD of SARS-CoV-2 Omicron variant result in stronger binding to human ACE2 receptor
The COVID-19 pandemic caused by the SARS-CoV-2 virus has led to more than 270 million
infections and 5.3 million of deaths worldwide. Several major variants of SARS-CoV-2 have …
infections and 5.3 million of deaths worldwide. Several major variants of SARS-CoV-2 have …
[HTML][HTML] A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …
generating pathways and rate constants for rare events such as protein folding and protein …
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
Predicting interactions between proteins and other biomolecules solely based on structure
remains a challenge in biology. A high-level representation of protein structure, the …
remains a challenge in biology. A high-level representation of protein structure, the …
ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome
Vaccines derived from chimpanzee adenovirus Y25 (ChAdOx1), human adenovirus type 26
(HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe …
(HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe …