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dockECR: Open consensus docking and ranking protocol for virtual screening of small molecules
(Elsevier Science Inc., 2021-12-15)
The development of open computational pipelines to accelerate the discovery of treatments for emerging diseases allows finding novel solutions in shorter periods of time. Consensus molecular docking is one of these approaches, ...
High-Throughput Docking Using Quantum Mechanical Scoring
(Frontiers Media, 2020-04)
Today high-throughput docking is one of the most commonly used computational tools in drug lead discovery. While there has been an impressive methodological improvement in docking accuracy, docking scoring still remains ...
Exponential consensus ranking improves the outcome in docking and receptor ensemble docking
(Nature Publishing Group, 2019-03)
Consensus-scoring methods are commonly used with molecular docking in virtual screening campaigns to filter potential ligands for a protein target. Traditional consensus methods combine results from different docking ...
An efficient use of X-ray information, homology modeling, molecular dynamics and knowledge-based docking techniques to predict protein-monosaccharide complexes
(Oxford University Press, 2018-11)
Unraveling the structure of lectin-carbohydrate complexes is vital for understanding key biological recognition processes and development of glycomimetic drugs. Molecular Docking application to predict them is challenging ...
Current trends in molecular modeling methods applied to the study of cyclodextrin complexes
(Springer, 2018-02)
In this review the authors present an overview of different molecular modeling campaigns dealing with the study and characterization of cyclodextrins (CDs) inclusion complexes with applicability to diverse biomedical and ...
Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase
(Springer, 2015)
The goal of this study was to identify neuraminidase (NA) residue mutants from human influenza AH1N1 using sequences from 1918 to 2012. Multiple alignment studies of complete NA sequences (5732) were performed. Subsequently, ...
Outside-binding site mutations modify the active site's shapes in neuraminidase from influenza A H1N1
(Wiley, 2013)
The recent occurrence of 2009 influenza A (H1N1) pandemic as well as others has raised concern of a far more dangerous outcome should this virus becomes resistant to current drug therapies. The number of clinical cases ...
Solvent structure improves docking prediction in lectin-carbohydrate complexes
(Oxford University Press, 2013-02)
Recognition and complex formation between proteins and carbohydrates is a key issue in many important biological processes. Determination of the three-dimensional structure of such complexes is thus most relevant, but ...
Correlation between initial biodegradability determined by docking studies and structure of alkylbenzene sulfonates: A new tool for intelligent design of environmentally friendly anionic surfactants
(Elsevier, 2020-08)
Gray water constitutes an important fraction of total wastewater. Some of the most problematic compounds in gray water are the anionic surfactants used as an ingredient for domestic and industrial soaps and detergents. The ...
Mapping the neurosteroid binding sites on glycine receptors
(Pergamon-Elsevier Science Ltd, 2019-09)
Glycine is a major inhibitory neurotransmitter in the CNS, where it modulates both sensory and motor transduction throughout its binding to glycine receptors (GlyRs), pentameric chloride channels that share structural and ...