The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on underexplored regions of configuration space while maintai...

Organophosphophorus compounds (OP) has been widely used as pesticides and as warfare nerve agents. They act by phosphorylating the hydroxyl group of the Ser 203 residue of the Acetylcholinesterase (AChE) active site, inhibiting its catalytic activity, causing the cholinergic Syndrome [1]. Currently, the OP poisoning treatment consists in the use of reactivators, for example oximes, a class of c...

In order to better understand the origin of life and the production of artificial living organisms and programmable nano-biorobots we used ab initio quantum mechanical (QM) Hartree-Fock (HF), density functional theory (DFT), QM semiempirical PM3 [1, 2} and molecular dynamics (MD) NAMD, GROMACS and CHARMM simulations [3-5] to investigate various bioorganic systems of artificial minimal living or...

Redox reaction of inorganic sulphur compound is very essential to maintain a global sulphur cycle. Certain experimental evidences suggest that gamma-proteobacterial Acidothiobacillus thiooxidans; lacking the sulphur-oxidizing (sox) operon, has an alternative thiosulphate oxidation pathway. Dox operon having essentially participating proteins; DoxD and DoxA serves as the central players for this...

microtubules, the active filaments with tubular shapes, play important roles in a wide range of cellular functions, including structural supports, mitosis, cytokinesis, and vesicular transport, which are essential for the growth and division of eukaryotic cells. finding properties of microtubules is one of the main concerns of scientists. this work helps to obtain mechanical properties of micro...

Insulin-like growth factor 1 receptor (IGF1R) is an attractive drug target for cancer therapy and research on IGF1R inhibitors has had success in clinical trials. A particular challenge in the development of specific IGF1R inhibitors is interference from insulin receptor (IR), which has a nearly identical sequence. A few potent inhibitors that are selective for IGF1R have been discovered experi...

Here, we describe the mechanism of diphenyl α-aminoalkylphosphonate ester derivatives as potent inhibitors of prostate-specific antigen (PSA), a likely protease responsible for the advancement of prostate tumor progression. The AutoDock 4.2 molecular docking suite was utilized to model covalent and noncovalent binding of this class of inhibitors to predict crystallographic poses and compare exp...

With the increase of available computational power and improvements in simulation algorithms, alchemical molecular dynamics based free energy calculations have developed into routine usage. To further facilitate the usability of alchemical methods for amino acid mutations, we have developed a web based infrastructure for obtaining hybrid protein structures and topologies. The presented webserve...

pH is an important parameter in condensed-phase systems, because it determines the protonation state of titratable groups and thus influences the structure, dynamics, and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fixed and cannot adapt to changes of the local environment. Here, we present ...

The use of beta solenoid proteins as functionalizable, nanoscale, self-assembling molecular building blocks may have many applications, including templating the growth of wires or higher-dimensional structures. By understanding their mechanical strengths, we can efficiently design the proteins for specific functions. We present a study of the mechanical properties of seven beta solenoid protein...