Glucagon-like peptide-1 (GLP-1) is a promising target for diabetes mellitus (DM) therapy and reduces the occurrence of diabetes due to obesity. However, GLP-1 will be hydrolyzed soon by the enzyme dipeptidyl peptidase-4 (DPP-4). We tried to design small molecular drugs for GLP-1 receptor agonist from the world's largest traditional Chinese medicine (TCM) Database@Taiwan. According to docking re...

Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD) trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify dif...

Background: Protein flexibility, which has been referred as a dynamic behavior has various roles in proteins’ functions. Furthermore, for some developed tools in bioinformatics, such as protein-protein docking software, considering the protein flexibility, causes a higher degree of accuracy. Through undertaking the present work, we have accomplished the quantification plus analysis of the varia...

MOTIVATION The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of experimental and theoretical work on protein dynamics. Further insight into the dynamics-function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The ...

Sirtuins family are a Nicotinamide Adenine Dinucleotide (NAD+) dependent histone deacetylase enzyme. have been implicated in the pathogenesis of various diseases including cancer, neurological disorders and metabolic syndromes, hence sirtuins appointed as promising therapeutic target for diseases, by regulating its activity small molecules modulators. The indole containing selisistat (EX-527) d...

Summary Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, ...

The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are ...

The discovery of antibiotics initiated the era drug innovation and implementation for human animal health. Very soon, antibiotic resistance started evolving due to over-prescription heavy usage drugs leading deleterious side effects. However, using plant extracts or medicinal plants has emerged as a new approach dealing with current problem. One such Sisymbrium irio L. is widely used in Unani t...

PyMOL (http://pymol.org) is an open-source software package designed for molecular graphics visualization and modelling. The PyMOL code-base is written in the C programming language, and much of the higher-level, useraccessible functionality is coded in Python. This software engineering design endows PyMOL with a rich Python application programming interface (API), which end-users can utilize f...

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacilluszalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed diff...