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Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case.
A conformational selection method, based on hydrogen bond (Hbond) network analysis, has been designed in order to rationalize the configurations sampled using molecular dynamics (MD), which areExpand
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Study of the interactions between Edaglitazone and Ciglitazone with PPAR&ggr; and their antiplatelet profile
ABSTRACT Peroxisome proliferator‐activated receptor &ggr; (PPAR&ggr;) is a ligand‐activated transcription factor with an important role in lipid metabolism, inflammation and cardiovascular diseases.Expand
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Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations
TLDR
We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. Expand
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Computational study of the binding orientation and affinity of PPARγ agonists: inclusion of ligand-induced fit by cross-docking
The peroxisome proliferator-activated receptors (PPARs) comprise a family of three nuclear receptor isoforms (γ, β/δ, α) which are key regulators of metabolism and inflammation. A series of potentExpand
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HQSAR and molecular docking studies of furanyl derivatives as adenosine A2A receptor antagonists
Structure- and ligand-based computational design strategies were used to understand the molecular requirements of furanyl derivatives 2-(furan-2-yl)-[1,2,4]triazolo[1,5-f]pyrimidin-5-amines (TfPAs),Expand
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Halogen bonding in drug-like molecules: a computational and systematic study of the substituent effect
Halogen bonding (XB) is a noncovalent interaction that has been increasingly used in molecular recognition, and more recently, in protein–ligand binding. We have studied and quantified, using densityExpand
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A2EPG: A new software for the analysis of electrical penetration graphs to study plant probing behaviour of hemipteran insects
TLDR
This article introduces A2EPG, a new software application capable of automatically analyse signals derived from the electrical penetration graphs (EPG), a technique widely used to monitoring the plant probing behaviour of hemipterean insects. Expand
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Docking and quantitative structure–activity relationship of bi-cyclic heteroaromatic pyridazinone and pyrazolone derivatives as phosphodiesterase 3A (PDE3A) inhibitors
PDE3s belong to the phosphodiesterases family, where the PDE3A isoform is the major subtype in platelets involved in the cAMP regulation pathway of platelet aggregation. PDE3A inhibitors have beenExpand
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