Introduction to Molecular Dynamics simulations theory

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Introduction to Molecular Dynamics simulations theory

Credit: Biomedical Research Foundation, Academy of Athens

Membrane protein tutorial with GROMACS

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Membrane protein tutorial with GROMACS

Credit: Biomedical Research Foundation, Academy of Athens

Molecular Dynamics Simulations of BPTI in Vacuum

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Molecular Dynamics Simulations of BPTI in Vacuum

Credit: Biomedical Research Foundation, Academy of Athens

Molecular Dynamics simulations of lysozyme in water

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Molecular Dynamics simulations of lysozyme in water

Credit: Biomedical Research Foundation, Academy of Athens

Tutorial 1.Simulation of a coarse grained DNA molecule in explicit solvent

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Tutorial 1. Simulation of a coarse grained DNA molecule in explicit solvent

Credit: Biomedical Research Foundation, Academy of Athens

Tutorial 2. Hybrid solvation: Plugging SIRAH solvent to your atomistic system

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Tutorial 2. Hybrid solvation: Plugging SIRAH solvent to your atomistic system

Credit: Biomedical Research Foundation, Academy of Athens

Tutorial 3. Simulation of coarse grained proteins in explicit solvent

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Tutorial 3. Simulation of coarse grained proteins in explicit solvent

Credit: Biomedical Research Foundation, Academy of Athens

Tutorial 4. Out of the box simulations of closed circular DNA

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Tutorial 4. Out of the box simulations of closed circular DNA

Credit: Biomedical Research Foundation, Academy of Athens

Protein-Small-Organic-Molecules-Interaction: PSOMI

PSOMI Description: PSOMI application connects pure theoretical and practical organic chemistry research with practical application and usage of newly synthesized organic molecules. So far newly synthesized molecules or group of molecules have never been tested for biological activity. The results of research will be of great importance for the understanding of ligand-receptor in simulated “live” system.

PSOMI training material: The following file provides a description of the PSOMI workflow

PSOMI Workflow

Thermodynamic stability of DNA/DNA and RNA/DNA duplexes of entire genomes of eukaryotic organisms: THERMOGENOME

THERMOGENOME Description: THERMOGENOME application provides study on how thermodynamic pattern of the genome influence fundamental processes of the cell such as transcription and RNA processing. Results could show why particular mutations alter RNA processing and lead to genetic diseases.

THERMOGENOME training material: The following document provides a description on the THERMOGENOME application.

THERMOGENOME execution of the Perl Script: description

AFMM

AFMM Description: AFMM provides an automated platform with which the users can generate parameters for modeling small molecules with Molecular Dynamics simulations. The method used fits the molecular mechanics potential function to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. The program optimizes an initial parameter set (either pre-existing or using chemically-reasonable estimation) by iteratively changing them until the optimal fit with the reference set is obtained. By implementing a Monte Carlo-like algorithm to vary the parameters, the tedious task of manual parameterization is replaced by an efficient automated procedure. The program is best suited for optimization of small rigid molecules in a well-defined energy minimum, for which the harmonic approximation to the energy surface is appropriate for describing the intra-molecular degrees of freedom.

Due to the abundance of organic molecules, no parameters have been created for the full chemical space. Thus, there is a great need for molecule parameterization before proceeding to Molecular Dynamics calculations. AFMM allows users to access parameters for their Molecular Dynamics simulation of small organic molecules that can be used as drugs or materials.

AFMM Training Material: The following file provides a tutorial on AFMM

AFMM Tutorial

NANO-Crystal

NANO-Crystal Description: NANO-Crystal is a web-based tool, is implemented for the construction of spherical nanoparticles of a given radius.
More specifically, our goal is to find the number and the Cartesian coordinates of smaller spheres that fit on the surface of the nanoparticle and visualize the output morphology. The home page menu allows two selections for the user:

• the radius of the nanosphere (nm), and
• (ii) the radius of smaller spheres (nm), that will cover the surface of the nanoparticle

The program computes the number of smaller spheres that fit on the bigger surface and the user can download their Cartesian coordinates (output format .xyz). The program code is implemented using PHP server-side scripting language, which is embedded into the HTML and CSS code. JQuery, a cross-platform JavaScript library, is also used. For local host of the webpage tool, the Wamp server is used. Moreover, we have developed a crystal computational morphology toolbox for constructing and modeling different crystal nanoparticle shapes. We use computational approaches for computing the macroscopic morphology of any periodic crystal by forming different shapes based on Miller indices and the distance measure from the center of the crystal and visualizing the resulting crystal. That crystal is a polyhedron that is created as the intersection of multiple polyhedra and individual planes via the steps that follows. This tool is planned to be imported in the NANO-Crystal webserver within 2017.
This tool enables users to construct spherical nanoparticles. Morevoer, within 2017 we will be importing our new code which enables the user to construct different crystal nanoparticle shapes based on Miller indices and the distance measure from the center of the crystal.

NANO-Crystal Training Material: The following file provides a tutorial on NANO-Crystal

NANO-Crystal Tutorial

Subtract

Subtract Description: Subtract is an online tool that can calculate the volume of a binding site found in a protein. Subtract accepts an atom selection in the form of a PDB file and computes the three-dimensional convex hull of the atoms points with the help of SciPy library. The next step of the algorithm is to compute the volume of the convex hull and the volume of the atoms that are included in the solid based on their van der Waals radii. The subtraction of those two volumes yields the volume of the investigated cavity. The algorithm computes cavity volumes of trajectory frames in parallel for maximum efficiency and speed. It requires minimal usage of memory due to the fact that it follows a buffering strategy of reading file chunks and therefore there is no need to load the entire file into memory. There is a wide support of trajectory formats like Gromacs trajectory files and multi-model PDB files due to its dependency to the MDTraj library.
The measurements are evaluated for statistical significance using Wilcoxon Signed-Rank test and had their null hypothesis rejected (p-value < 0.005). Subtract is a tool that has been created to solve the problem of accurate measurement of the protein binding sites, and works both for crystal structures downloaded from the Protein Data Bank and for protein structures arising from Molecular Dynamics simulations trajectories.

Subtract Training Material: The following link provides a tutorial on Subtract

Subtract Tutorial