Application-level Services for the Life Sciences community include online services and workflows able to pre-process and visualize data in an automated manner.
The following services are available to the community:
ChemBioServer
ChemBioServer is a web-application for effectively mining and filtering chemical compounds used in drug discovery. ChemBioServer allows for pre-processing of compounds prior to an in silico screen, as well as for post-processing of top-ranked molecules resulting from a docking exercise with the aim to increase the efficiency and the quality of compound selection that will pass to the experimental test phase. It provides researchers with the ability to:
- browse and visualize compounds along with their properties
- filter chemical compounds for a variety of properties such as steric clashes and toxicity
- apply perfect match substructure search
- cluster compounds according to their physicochemical properties providing representative compounds for each cluster
- build custom compound mining pipelines
- quantify through property graphs the top-ranking compounds in drug discovery procedures.
AFMM
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.
NANO-Crystal
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:
- (i) 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.
Subtract
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.
DICOM
"DICOM Network" provides access to investigations for medical staff with the appropriate access rights and as well as patients to the personal radiography investigations. Nowadays the system collects and processes more than 500 gigabytes of data per month. The system is based on Data Storage and Data Processing components distributed between different processing units and storages, which could be customized using specific interfaces. VISEEM integration connects national DICOM Network application, that it is containing existing DICOM Portal http://dicom.md/, with the DICOM Portal installed on VI-SEEM platform resources. DICOM DATA Interface grants the interconnectivity for different users of the both portals and allows displaying DICOM investigations using both portals interfaces. Public DICOM Server grants possibility for any VI-SEEM platform member to pull and retrieve the investigations from DICOM Network application and use the developed facilities based on configured access rules. VI-SEEM platform will offer possibility to install and configure publically available DOCOM Portal that can be used by any interested institutions to store, access and share medical images. Setting up public DICOM Portal instance will increase the level of access to DICOM investigations and will help to promote DICOM Network services to regional medical research and practicing community.