INTERNSHIP PROGRAM OF BIODISCOVERY GROUP

INTERNSHIP PROGRAM OF BIODISCOVERY GROUP - Explara
Apr 3, 2017 - Dec 31, 2017 09:00 PM - 11:00 PM
BioDiscovery Group
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BioDiscovery Group Lifesciences is offering internship of 30, 45 & 60 Days in following topics. These internships are offered ONLINE and ONSITE (at our Bengaluru Office, Karnataka, India) throughout the year. The category/area of internships are:

  • Chemoinformatics Approaches for Drug Discovery Technology and Molecular Simulations.
  • Immunoinformatics Approaches for Vaccine Design.
  • Computer Aided Herbal Drug Discovery for Edible Vaccines.
  • Next Generation Sequencing.
  • Molecular Biology and Genetic Engineering.
  • Homology Modelling.

The subtopics under each category are as follows:

Chemoinformatics Approaches for Drug Discovery Technology and Molecular Simulations

  • In-silico generation of ligands by ChemSketch
  • Pharmacophore Detection.
  • Modification of Ligand.
  • Conversion of Mol files to Pdb files by Open Babel
  • Homology Modelling
  • Protein optimization & Energy Minimization by SPDBV
  • Molecular Docking by MGL Tools | Creation of Grid Parameter & Dock Parameter files by AutoDock Software
  • Running the Docking Algorithm by Cygwin
  • Selection of potent inhibitors on the basis of binding energies(delta G) and Lipinski's Rule of 5
  • Creating docking complex
  • Structure Analysis- Protein & ligand complex H-bond interaction by UCSF Chimera
  • Drug Optimisation
  • Making a protein structure file.
  • Solvating the protein in a water box- parameter generation for the protein or the small molecule
  • Adding ions to the solvated protein.
  • NAMD configuration file.
  • Minimization and equilibration.
  • Simulations parameters and running the simulations.
  • Analysis of the simulations.

Immunoinformatics Approaches for Vaccine Design

  • Introduction to Immunoinformatics
  • Role of Immunoinformatics in advance medicine field.
  • Practical overview
  • Immunome browser
  • Antigenic protein retrieval
  • Functional analysis
  • Introduction to computational vaccine design.
  • Types of vaccine design and application.
  • Practical overview.
  • Case study
  • Retrieval of sequence
  • Antigenicity prediction
  • Allergy prediction
  • Functional analysis
  • Protein structure analysis
  • Modeling
  • Antigen active site
  • Population coverage
  • Visualization of antibody

Computer Aided Herbal Drug Discovery for Edible Vaccines

  • Introduction to CADD
  • Applications of CADD
  • Bibliographic Search
  • Plant Databases
  • Plant Genomics
  • Plant Proteomics
  • Pharmacophore Identification
  • Modification of Lead Molecule
  • Protein Structure Retrieval
  • Molecular Modelling
  • Molecular Docking
  • ADMEAnalysis
  • Comparison of Results- Rule Of 5 & QSAR

Next Generation Sequencing

  • Basic Terminologies
  • Introduction to file types in NGS
  • Database and file formats in NGS
  • NCBI Genomics Library
  • NCBI Resources Used In Next Generation Sequencing
  • Blasting into SRA
  • Preprocessing of raw reads: quality control (FastQC), adapter clipping, quality trimming
  • Mapping output (SAM/BAM format)
  • Retrieving sequence from SRA (NCBI toolkit)
  • Raw sequence files (FASTQ format)
  • Finding NGS data from PUBMED SRA link
  • DNA and RNA-seq NGS read alignment
  • Visualization of mapped reads
  • Germline variant calling
  • Somatic variant calling and de novo mutation
  • Variant Filtering and annotation
  • Variant association and prioritization
  • Big Data Analysis and visualization

Molecular Biology and Genetic Engineering

  • Introduction to molecular biology and genetic engineering.
  • Application of molecular biology and genetic engineering in bioinformatics.
  • Promotor analysis in genome.
  • Structural annotation.
  • Functional annotation
  • Active site prediction
  • Single nucleotide polymorphism.
  • Mutation
  • Homology modeling.
  • Model validation.
  • Visualization of model

Homology Modelling

The term "homology modelling", also known as comparative modelling or template-based modelling. It refers to modelling a protein 3D structure using a known experimental structure of a homologous protein (the template). Structural information is always of great assistance in the study of protein function, dynamics, interactions with ligands and other proteins. The "low-resolution" structure provided by homology modelling contains sufficient information about the spatial arrangement of important residues in the protein and may guide the design of new experiments, for example site-directed mutagenesis. Even within the pharmaceutical industry homology modelling can be valuable in structure-based drug discovery and drug design.

TOPICS INCLUDED

  • Basic Modelling
  • Advanced Modelling
  • Iterative Modelling
  • Difficult Modelling

TOOLS

  • Modeller
BioDiscovery Group, 24th Main Road 1st Phase,J P Nagar, Bengaluru, Karnataka, India
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