Dynamic docking: a paradigm shift in computational drug discovery
Molecular docking is the methodology of choice for studying in silico protein-ligand binding
and for prioritizing compounds to discover new lead candidates. Traditional docking …
and for prioritizing compounds to discover new lead candidates. Traditional docking …
Computer-aided drug design methods
Computational approaches are useful tools to interpret and guide experiments to expedite
the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based …
the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based …
Driving structure-based drug discovery through cosolvent molecular dynamics: Miniperspective
Identifying binding hotspots on protein surfaces is of prime interest in structure-based drug
discovery, either to assess the tractability of pursuing a protein target or to drive improved …
discovery, either to assess the tractability of pursuing a protein target or to drive improved …
The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins
FTMap is a computational map** server that identifies binding hot spots of
macromolecules—ie, regions of the surface with major contributions to the ligand-binding …
macromolecules—ie, regions of the surface with major contributions to the ligand-binding …
Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma
Diffuse large B cell lymphomas (DLBCLs) arise from proliferating B cells transiting different
stages of the germinal center reaction. In activated B cell DLBCLs (ABC-DLBCLs), a class of …
stages of the germinal center reaction. In activated B cell DLBCLs (ABC-DLBCLs), a class of …
In silico identification of a β2-adrenoceptor allosteric site that selectively augments canonical β2AR-Gs signaling and function
Activation of β2-adrenoceptors (β2ARs) causes airway smooth muscle (ASM) relaxation and
bronchodilation, and β2AR agonists (β-agonists) are front-line treatments for asthma and …
bronchodilation, and β2AR agonists (β-agonists) are front-line treatments for asthma and …
Molecular dynamics in mixed solvents reveals protein–ligand interactions, improves docking, and allows accurate binding free energy predictions
One of the most important biological processes at the molecular level is the formation of
protein–ligand complexes. Therefore, determining their structure and underlying key …
protein–ligand complexes. Therefore, determining their structure and underlying key …
Molecular simulations with solvent competition quantify water displaceability and provide accurate interaction maps of protein binding sites
Binding sites present well-defined interaction patterns that putative ligands must meet.
Knowing them is essential to guide structure-based drug discovery projects. However …
Knowing them is essential to guide structure-based drug discovery projects. However …
Rapid and accurate estimation of protein–ligand relative binding affinities using site-identification by ligand competitive saturation
Predicting relative protein–ligand binding affinities is a central pillar of lead optimization
efforts in structure-based drug design. The site identification by ligand competitive saturation …
efforts in structure-based drug design. The site identification by ligand competitive saturation …
Structure-based design of potent iminosugar inhibitors of endoplasmic reticulum α-glucosidase I with anti-SARS-CoV-2 activity
SS Karade, EJ Franco, AC Rojas… - Journal of medicinal …, 2023 - ACS Publications
Enveloped viruses depend on the host endoplasmic reticulum (ER) quality control (QC)
machinery for proper glycoprotein folding. The endoplasmic reticulum quality control …
machinery for proper glycoprotein folding. The endoplasmic reticulum quality control …