In this investigation, the synthesis of 2-substituted pyrimidines by the reaction of benzofuranchalcones (3a-d) with urea, thiourea and guanidine hydrochloride was reported. The structuresof title compounds (4a-d), (5a-d) and (6a-d) were established on the basis of analyticaland spectral data. The synthesized compounds were screened for antimicrobial activityand molecular docking studies. Some ...

Flibanserin is a novel antagonist small molecule to treat the hypoactive sexual desire disorder (HSDD) in the premenopausal women. The present article is related to the structural and electronic properties study and docking analysis of the title compound with 5-hydroxytryptamine 2A (5-HT2A) serotonin receptor. To access these aims, the molecular structure of the said compound was optimized usin...

SUMMARY Herein, we present CONSRANK, a web tool for analyzing, comparing and ranking protein-protein and protein-nucleic acid docking models, based on the conservation of inter-residue contacts and its visualization in 2D and 3D interactive contact maps. AVAILABILITY AND IMPLEMENTATION CONSRANK is accessible as a public web tool at https://www.molnac.unisa.it/BioTools/consrank/. CONTACT rom...

Microbial Transglutaminase (MTgase) shows a wide specificity of action in its ability to interact with proteins from different families. Previous experimental data (in collaboration with BIOKER, POLARIS, Pula, Italy) demonstrated that MTGase interacts and transglutaminates the Granulocyte-Colony-StimulatingFactor (GCSF) at residue Q135. In this work this interaction is investigated through the ...

A newly developed statistical pair potential based on Distance-scaled Finite Ideal-gas REference (DFIRE) state is applied to unbound protein-protein docking structure selections. The performance of the DFIRE energy function is compared to those of the well-established ZDOCK energy scores and RosettaDock energy function using the comprehensive decoy sets generated by ZDOCK and RosettaDock. Despi...

With the advancement of novel techniques in drug discovery, various approaches have been used in the structure based drug designing. One of the most important strategies is molecular docking. The study of molecular docking and simulation deals with the intermolecular interaction of drug targets i.e. proteins, nucleic acids, lipids and ligands. The aim of molecular docking is to achieve an optim...

Loops connect regular secondary structures. In many instances, they are known to play crucial biological roles. To bypass the limitation of secondary structure description, we previously defined a structural alphabet composed of 16 structural prototypes, called Protein Blocks (PBs). It leads to an accurate description of every region of 3D protein backbones and has been used in local structure ...

The inclusion of receptor flexibility in protein-ligand docking experiments has become a major research interest in drug discovery [1,2]. One of the possible methods applied is the use of multiple discrete protein conformations, so called ensemble docking [3,4]. With computational techniques like Molecular Dynamics (MD) a large number of different conformations can be generated, not all of whic...

MOTIVATION The limited success rate of protein-protein docking procedures is generally attributed to structure differences between the bound and unbound states of the molecules. Herein we analyze a large dataset of protein-protein docking results and identify additional parameters that affect the performance of docking procedures. RESULTS We find that the distinction between nearly correct mo...

In this research work, a proficient method has been developed for the preparation of novel N-((2-chloroquinolin-3-yl) methylene)-4-methylbenzenamine derivatives from 2-chloroquinoline-3-carbaldehyde derivatives and p-toluidine in ethanol as solvent and using catalytic amount of acetic acid under reflux conditions to obtain desired products in good yields. The identification of all the synthesiz...