Here we list a whole set of topics that you could consider when considering Life Science Software and tools.
- Molecular Dynamics Simulations
- Computer Aided Drug Design
- Next Generation Sequencing Data Analysis
- Medical Image Processing
Molecular Dynamics Simulations
General Training Material
Introduction to Molecular Dynamics simulations theory
To view the material please click on the link below:
Introduction to Molecular Dynamics simulations theory
Credit: Biomedical Research Foundation, Academy of Athens
Membrane protein tutorial with GROMACS
To view the material please click on the link below:
Membrane protein tutorial with GROMACS
Credit: Biomedical Research Foundation, Academy of Athens
Molecular Dynamics Simulations of BPTI in Vacuum
To view the material please click on the link below:
Molecular Dynamics Simulations of BPTI in Vacuum
Credit: Biomedical Research Foundation, Academy of Athens
Molecular Dynamics simulations of lysozyme in water
To view the material please click on the link below:
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
To view the material please click on the link below:
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
To view the material please click on the link below:
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
To view the material please click on the link below:
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
To view the material please click on the link below:
Tutorial 4. Out of the box simulations of closed circular DNA
Credit: Biomedical Research Foundation, Academy of Athens
Vi-SEEM Applications
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
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.
Application Level Services
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
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
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
Computer Aided Drug Design
General Training Material
Principles of Computer-Aided Drug Design
To view the material please click on the link below:
Principles of Computer-Aided Drug Design
Credit: Biomedical Research Foundation, Academy of Athens
Vi-SEEM Applications
Conventional vs Novel Computer Assisted Drug Delivery: CNCADD
CNCADD Description: CNCADD application provides a comparison of conventional with novel models for computer assisted drug delivery simulation, using methodologies including molecular dynamics, statistical physics, and Monte Carlo.
CNCADD training material: The following document provides a description on the CNCADD application.
CNCADD: Calculation of the local mode fequencies description
For training purposes, the following link provides a Fortran code used for computing the partial autocorrelation function pACF of the time-derivative of the X-H bond length
Predicting Farnesoid X receptor (FXR) - inhibitor structures and affinities for computer-aided drug design within the D3R challenge: D3R
D3R Description: The scientific scope of D3R is 1. to enhance the predictability of ligand-protein binding pose prediction using computer-aided drug design and 2. to deliver guidelines for lead optimization using free energy perturbation calculations.
D3R training material: The following documents provide presentations on the two scientific scopes of D3R:
Presentation: Predicting ligand-protein binding poses in the D3R drug design competition
Presentation: Lead optimization predictions in the D3R drug design competition
Application Level Services
ChemBioServer
ChemBioServer Description: 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.
ChemBioServer Training Material: Below you can find tutorials for the ChemBioServer
Next Generation Sequencing Data Analysis
Vi-SEEM Applications
Next Generation Sequencing pipeline: NGS1
NGS1 Description: NGS1 application provides application of NGS technology and pipeline to address the identification of genetic mutations that cause rare diseases in families and of genetic variants that contribute to complex diseases such as autism and cancer.
NGS1 training material: The following document provides the best practices used
NGS1: guidelines for Next generation sequencing of human samples using Illumina NextSeq500 platform
Next Generation Sequencing Data Analysis: NGS2
NGS2 Description: Characterization of biomarkers using NGS data targeting improvement of non-invasive prenatal diagnosis methods and detection methods of genetic abnormalities in a noninvasive assay.
NGS2 training material: The following document provides the best practices used
NGS2: A guide with examples on how to perform alignment of NGS data and avoid various pitfalls.
Medical Image Processing
Vi-SEEM Applications
Classification of cancer cells: CCC
CCC Description: CCC provides an advanced approach for x-ray images in the context of signal processing, enabling medical users to diagnosis automatically cancer cells.
CCC training material: The following document provides a basic description on the CCC application
and the following document provides a presentation on how one can use the CCC software.
Application Level Services
Visualization & Medical Image Processing DICOM Network: DICOM
DICOM Description: "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.
DICOM training material: The following document provides a description on the DICOM application