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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 ...
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 ...
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, ...
Identification of renin inhibitors peptides from amaranth proteins by docking protocols
(Elsevier, 2020-01)
The objective of this work was to develop a new protocol to predict with greater confidence peptides as potential inhibitors of the renin enzyme. For this, free, friendly and rigorous servers developed specifically for ...
Strengths and Weaknesses of Docking Simulations in the SARS-CoV-2 Era: The Main Protease (Mpro) Case Study
(American Chemical Society, 2021-07)
The scientific community is working against the clock to arrive at therapeutic interventions to treat patients with COVID-19. Among the strategies for drug discovery, virtual screening approaches have the capacity to search ...
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 ...
Ligand and decoy sets for docking to G protein-coupled receptors
(American Chemical Society, 2012-01)
We compiled a G protein-coupled receptor (GPCR) ligand library (GLL) for 147 targets, selecting for each ligand 39 decoy molecules, collected in the GPCR Decoy Database (GDD). Decoys were chosen ensuring a ligand-decoy ...
AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions
(Oxford University Press, 2019-10)
Summary: The performance of docking calculations can be improved by tuning parameters for the system of interest, e.g. biasing the results towards the formation of relevant protein-ligand interactions, such as known ligand ...
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 ...
Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking
(Springer, 2021-11)
Screening already approved drugs for activity against a novel pathogen can be an important part of global rapid-response strategies in pandemics. Such high-throughput repurposing screens have already identifed several ...