Introduction : The innate immune system as the first line of defense against the pathogens recognizes pathogen-associated molecular patterns (PAMPs) by Toll-Like Receptors (TLRs). Interaction of bacterial PAMPs by TLRs results in activation of innate and acquired immunity. FimH adhesin, a minor component of type 1 fimbriae encoded by Uropathogenic Escherichia coli (UPEC) is a PAMP of TLR4 tha...

It is well known that computer-aided docking of large ligands, with many rotatable bonds, is extremely difficult. AutoDock is a widely used docking program that can dock small ligands, with upto 5 or 6 rotatable bonds, accurately and quickly. Docking of larger ligands, however, is not very accurate and is computationally expensive. In this paper we present an AutoDock-based incremental docking ...

The results from reiterated docking experiments may be used to evaluate an empirical vibrational entropy of binding in ligand-protein complexes. We have tested several methods for evaluating the vibrational contribution to binding of 22 nucleotide analogues to the enzyme APS reductase. These include two cluster size methods that measure the probability of finding a particular conformation, a me...

in this report, we describe a procedure for in-silico design of a novel haloalkane dehalogenase protein that exhibits luciferase property which can be potentially used in biosensor applications. from a pdb blast search, the selected haloalkane dehalogenase (pdb code: 1ede) had a close structural homology with a lucifearse (pdb code: 2psj chain a) sharing an identity of 33%. initially, the amino...

an efficient synthesis of polyhydroquinoline derivatives is achieved via hantzsch condensation reaction between aldehydes, dimedone, ethyl acetoacetate and ammonium acetate in the presence of catalytic amount of sfhs in ethanol. this method gives remarkable advantages such as shorter reaction time, simple workup procedure and good to excellent yields. furthermore the catalyst can be recovered c...

Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the 168 proteins of the Mintseris Benchmark 2.0. On the one hand, we evaluated the quality of the in...

In the present study, the antimicrobial tests of patchouli oil were studied by using molecular docking technology and antimicrobial test in vitro. Five biological macromolecule enzymes, required by the bacteria in the process of biosynthesis were selected as target molecules. Five antibiotics benzylpenicillin, sulfadiazine, trimethoprim, rifampicin and ciprofloxacin, which are generally acknowle...

In the present study, the antimicrobial tests of patchouli oil were studied by using molecular docking technology and antimicrobial test in vitro. Five biological macromolecule enzymes, required by the bacteria in the process of biosynthesis were selected as target molecules. Five antibiotics benzylpenicillin, sulfadiazine, trimethoprim, rifampicin and ciprofloxacin, which are generally acknowle...

a series of 42 pyrazolo[4,3-h]quinazoline-3-carboxamides as multi-cyclin-dependent kinaseinhibitors regarded as promising antitumor agents to complement the existing therapies, wassubjected to a three-dimensional quantitative activity relationship (3d qsar). different qsarmethods, comparative molecular field analysis (comfa), comfa region focusing, andcomparative molecular similarity indices an...