Structure-based virtual screening for drug discovery: principles, applications and recent advances
Structure-based drug discovery (SBDD) is becoming an essential tool in assisting fast and
cost-efficient lead discovery and optimization. The application of rational, structure-based …
cost-efficient lead discovery and optimization. The application of rational, structure-based …
Next generation 3D pharmacophore modeling
Abstract 3D pharmacophore models are three‐dimensional ensembles of chemically
defined interactions of a ligand in its bioactive conformation. They represent an elegant way …
defined interactions of a ligand in its bioactive conformation. They represent an elegant way …
Role of molecular dynamics and related methods in drug discovery
Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …
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 …
[HTML][HTML] Exploring the computational methods for protein-ligand binding site prediction
J Zhao, Y Cao, L Zhang - Computational and structural biotechnology …, 2020 - Elsevier
Proteins participate in various essential processes in vivo via interactions with other
molecules. Identifying the residues participating in these interactions not only provides …
molecules. Identifying the residues participating in these interactions not only provides …
How beyond rule of 5 drugs and clinical candidates bind to their targets
BC Doak, J Zheng, D Dobritzsch… - Journal of medicinal …, 2016 - ACS Publications
To improve discovery of drugs for difficult targets, the opportunities of chemical space
beyond the rule of 5 (bRo5) were examined by retrospective analysis of a comprehensive …
beyond the rule of 5 (bRo5) were examined by retrospective analysis of a comprehensive …
Inside the human cancer tyrosine phosphatome
Members of the protein tyrosine phosphatase (Ptp) family dephosphorylate target proteins
and counter the activities of protein tyrosine kinases that are involved in cellular …
and counter the activities of protein tyrosine kinases that are involved in cellular …
Investigating cryptic binding sites by molecular dynamics simulations
Conspectus This Account highlights recent advances and discusses major challenges in
investigations of cryptic (hidden) binding sites by molecular simulations. Cryptic binding …
investigations of cryptic (hidden) binding sites by molecular simulations. Cryptic binding …
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
Motivation: A variety of pocket detection algorithms are now freely or commercially available
to the scientific community for the analysis of static protein structures. However, since …
to the scientific community for the analysis of static protein structures. However, since …
[HTML][HTML] Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization
The mutation and overexpression of the epidermal growth factor receptor (EGFR) are
associated with the development of a variety of cancers, making this prototypical …
associated with the development of a variety of cancers, making this prototypical …