Background: The gold standard for detection of bladder cancer is cystoscopy, which is an invasive and complicated procedure. Our study was conducted to find a tumor marker with high specificity, sensitivity, and accuracy for the diagnosis of bladder cancer. Methods: Serum samples were collected from 58 bladder cancer patients and 60 healthy control subjects. Levels of lipid-bound sialic acid...

By using different evaluation strategies, we systemically evaluated the performance of Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodologies based on more than 1800 protein-ligand crystal structures in the PDBbind database. The results can be summarized as follows: (1) for the one-protein-family/one-binding-lig...

We have applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method (J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, and D. A. Case, Journal of the American Chemical Society, 1998, Vol. 120, pp. 9401-9409) to study the interaction of an RNA aptamer with theophylline and its analogs. The MM-PBSA free energy analysis provides a reasonable absolute binding free energy...

The Incidence of childhood obesity and metabolic syndrome is increasing even in rural and semi-urban regions of India. Adipose tissue mass secretes several inflammatory proteins, which could potentially alter the metabolic processes, leading to several complications at the later stages of life. With limited studies on protein bound sialic acid (PBSA) as a marker of oxidative stress mediated inf...

Poly(butylene adipate-co-terephthalate) (PBAT) and poly(butylene succinate-co-adipate) (PBSA) blend films were prepared with different contents of a multifunctional epoxide chain extender Joncryl ADR-4468 (ADR) or benzoyl peroxide (BPO). The long-chain-branching (LCB) introduced by ADR branched/crosslinked entanglement induced BPO increased melt elasticity, viscosity compatibility, as indicated...

With the rapid development of computational techniques and hardware, more rigorous and precise theoretical models have been used to predict the binding affinities of a large number of small molecules to biomolecules. By employing continuum solvation models, the MM/GBSA and MM/PBSA methodologies achieve a good balance between low computational cost and reasonable prediction accuracy. In this stu...

End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using...

Polylactide/poly[(butylene succinate)-co-adipate] (PLA/PBSA)-organoclay composites were prepared via melt compounding in a batch mixer. The weight ratio of PLA to PBSA was kept at 70:30, while the weight fraction of the organoclay was varied from 0 to 9%. Small angle X-ray scattering patterns showed slightly better dispersion in PBSA than PLA, and there was a tendency of the silicate layers to ...

The pH-driven opening and closure of beta-lactoglobulin EF loop, acting as a lid and closing the internal cavity of the protein, has been studied by molecular dynamics (MD) simulations and free energy calculations based on molecular mechanics/Poisson-Boltzmann (PB) solvent-accessible surface area (MM/PBSA) methodology. The forms above and below the transition pH differ presumably only in the pr...

Thermoplastic starch/butyl glycol ester copolymer/polylactic acid (TPS/PBSA/PLA) biodegradable composites were prepared by melt-mixing. The structure, microstructure, mechanical properties and heat resistance of the TPS/PBSA/PLA studied Fourier-transform infrared spectrometry (FTIR), scanning electron microscopy (SEM), tensile test thermogravimetry tests, respectively. results showed that PBSA ...