Ensemble docking in drug discovery
Ensemble docking corresponds to the generation of an" ensemble" of drug target
conformations in computational structure-based drug discovery, often obtained by using …
conformations in computational structure-based drug discovery, often obtained by using …
Multiscale methods in drug design bridge chemical and biological complexity in the search for cures
RE Amaro, AJ Mulholland - Nature Reviews Chemistry, 2018 - nature.com
Drug action is inherently multiscale: it connects molecular interactions to emergent
properties at cellular and larger scales. Simulation techniques at each of these different …
properties at cellular and larger scales. Simulation techniques at each of these different …
Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery
Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …
Making it rain: cloud-based molecular simulations for everyone
We present a user-friendly front-end for running molecular dynamics (MD) simulations using
the OpenMM toolkit on the Google Colab framework. Our goals are (1) to highlight the usage …
the OpenMM toolkit on the Google Colab framework. Our goals are (1) to highlight the usage …
Computational molecular interaction between SARS-CoV-2 main protease and theaflavin digallate using free energy perturbation and molecular dynamics
Our objective was to identify the molecule which can inhibit SARS-CoV-2 main protease and
can be easily procured. Natural products may provide such molecules and can supplement …
can be easily procured. Natural products may provide such molecules and can supplement …
Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
Exascale computing has been a dream for ages and is close to becoming a reality that will
impact how molecular simulations are being performed, as well as the quantity and quality of …
impact how molecular simulations are being performed, as well as the quantity and quality of …
Designing a multi-epitope vaccine against Chlamydia pneumoniae by integrating the core proteomics, subtractive proteomics and reverse vaccinology-based …
Chlamydia pneumoniae, a pneumonia causing specie belonging to chlamydia bacterium. C.
pneumonia is considered as a leading cause of pneumonia. Apart from that, C. pneumoniae …
pneumonia is considered as a leading cause of pneumonia. Apart from that, C. pneumoniae …
Continuous evaluation of ligand protein predictions: a weekly community challenge for drug docking
Docking calculations can accelerate drug discovery by predicting the bound poses of
ligands for a targeted protein. However, it is not clear which docking methods work best …
ligands for a targeted protein. However, it is not clear which docking methods work best …
Improving the efficiency of ligand-binding protein design with molecular dynamics simulations
Custom-designed ligand-binding proteins represent a promising class of macromolecules
with exciting applications toward the design of new enzymes or the engineering of …
with exciting applications toward the design of new enzymes or the engineering of …
Fighting viruses with computers, right now
MR Machado, S Pantano - Current Opinion in Virology, 2021 - Elsevier
The synergistic conjunction of various technological revolutions with the accumulated
knowledge and workflows is rapidly transforming several scientific fields. Particularly …
knowledge and workflows is rapidly transforming several scientific fields. Particularly …