The Protein Structure Prediction (PSP) problem is concerned about the prediction of the native tertiary structure of a protein in respect to its amino acids sequence. PSP is a challenging and computationally open problem. Therefore, several researches and methodologies have been developed for it. In this way, developers are working to integrate frameworks in order to improve their capabilities ...

UNLABELLED Atomistic molecular dynamics simulation is a promising technique to investigate the energetics and dynamics in the protein-surface adsorption process which is of high relevance to modern biotechnological applications. To increase the chance of success in simulating the adsorption process, favorable orientations of the protein at the surface must be determined. Here, we present ProtPO...

Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and...

Reverse turns play an important role in protein folding, molecular recognition and in eliciting immune response. While sequence determinants of reverse turns are known, not much is known about their energetics. In this paper we have investigated the thermodynamics of a reverse turn sequence YPGDV, an experimentally well characterized turn sequence, using molecular dynamics simulations performed...

Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPT-GSHMC, combines Andersen barostat with GSHMC to enable molecular simulations in the environment natural for biological applications, namely, at constant pressure and constant temperature. Gener...

The Martini model, a coarse-grained force field for molecular dynamics simulations, has been around nearly two decades. Originally developed lipid-based systems by the groups of Marrink and Tieleman, model over years extended as community effort to current level general-purpose field. Apart from obvious benefit reduction in computational cost, popularity is largely due systematic yet intuitive ...

UNLABELLED In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds...

Coronavirus 19 (COVID-19) is still a global health issue to date, SARS-CoV-2 novel coronavirus that responsible for this sickness. The receptor-binding domain of the virus associates with angiotensin-converting enzyme 2 (ACE-2) and allows enter human cells. Natural peptides such alpha-defensin are thought attach RBD prohibit it from engaging ACE-2. Molecular dynamics simulations using computati...

Kanker payudara menjadi salah satu jenis kanker dengan penderita terbanyak baik di dunia maupun Indonesia, Reseptor Estrogen Alfa (ER-α) target utama karena dapat mengatur transkripsi gen dan jalur persinyalan interseluler. Penelitian ini bertujuan untuk menganalisis afinitas kestabilan ikatan kompleks ligan senyawa turunan furanokumarin reseptor estrogen alfa. Metode yang digunakan secara in s...