Bioinformatics – STEM Skills Lab https://new.stemskillslab.com We make you thinkable Mon, 02 Jan 2023 07:18:01 +0000 en-US hourly 1 https://wordpress.org/?v=6.9.1 213064967 Nucleic Acids Modeling and Simulations https://new.stemskillslab.com/courses/nucleic-acids-modeling-and-simulations/ Mon, 02 Jan 2023 06:57:51 +0000 https://new.stemskillslab.com/?post_type=stm-courses&p=5177

Studying Nucleic acid modeling and simulations is essential for understanding the structure and function of DNA and RNA, which are critical biomolecules involved in many crucial biological processes. In addition, nucleic acid modeling and simulations study can provide students with several benefits, including:

  1. Improved understanding of biological processes: By studying nucleic acid modeling and simulations, students can gain a deeper understanding of how DNA and RNA function at the molecular level and how they are involved in various biological processes, such as gene expression and regulation.

  2. Practical skills in computational biology: Nucleic acid modeling and simulations require specialized software and computational techniques, which can help students develop practical skills in computational biology. These skills are in high demand in academia and industry.

  3. Opportunities for interdisciplinary research: Nucleic acid modeling and simulations involve integrating concepts and techniques from multiple disciplines, such as chemistry, biology, and computer science. This multidisciplinary nature can allow students to collaborate on research projects with researchers from different fields.

  4. Career opportunities: The demand for skilled professionals in nucleic acid modeling and simulations is growing as these techniques are increasingly used to study a wide range of biological problems. As such, students who study nucleic acid modeling and simulations may have good job prospects in academia, industry, and government research organizations.

Studying nucleic acid modeling and simulations can give students a deeper understanding of biological processes, practical skills in computational biology, opportunities for interdisciplinary research, and good career prospects.

Module – 6 months Nucleic Acids MODELING & SIMULATION
Topics

– Protein Data Bank (PDB), Nucleic Acid Data Bank (NDB) RCSB, UNIPROT

-Introduction to various sequence Databases

– Studying Sequence and 2D and 3D structure of DNA/RNA

-Learning Visualization tools (Rasmol and Pymol)

-Studying Various Motifs in RNA structures

– Analyzing H-bonding and Stacking between Nucleobases in RNA

– Modeling 3D structure of DNA/RNA

– Molecular Dynamics Simulations

– Simulation using GROMACS

-Analyzing Results

– Writing Report

 

Who can apply:

  • B.Tech. in (Biotechnology/ Industrial Biotechnology/ Bioinformatics/Material Sciences/Computer Sciences)
  • M.Sc. in (Biotechnology/Microbiology/Chemistry/Biochemistry/Bioinformatics/Life sciences/Material Sciences)
  • M.Tech. in (Biotechnology/Bioinformatics/ Industrial Biotechnology/Computer Sciences)
  • B.Pharmacy/ M.Pharmacy
 
]]> 5177 BIOMOLECULAR MODELING AND SIMULATIONS https://new.stemskillslab.com/courses/biomolecular-modeling-and-simulations/ Sun, 11 Dec 2022 03:50:33 +0000 https://new.stemskillslab.com/?post_type=stm-courses&p=5165
Module – 6 months Biomolecular Modelling and Docking
Topics – Protein Data Bank (PDB), RCSB, UNIPROT
– Studying Sequence, 2D, and 3D structure.-Learning Visualization tools (Rasmol and Pymol)
-Studying Receptor and ligand structure
– Learning Docking methods
– Hands-on training of Autodock and Haddock tool-Analyzing Interactions between Ligand-Receptor Docked structure
– Molecular Dynamics Simulations
– Simulation using GROMACS-Analyzing Results

Who can Apply for training?

B.Tech. in (Biotechnology/ Industrial Biotechnology/ Bioinformatics/Material Sciences/Computer Sciences)
M.Sc. in (Biotechnology/Microbiology/Chemistry/Biochemistry/Bioinformatics/Life sciences/Material Sciences)
M.Tech. in (Biotechnology/Bioinformatics/ Industrial Biotechnology/Computer Sciences)
B.Pharmacy/ M.Pharmacy

 
]]> 5165 Molecular Modeling and Drug Designing https://new.stemskillslab.com/courses/molecular-modeling-and-drug-designing/ Tue, 08 Feb 2022 12:29:52 +0000 http://lmsdemo.loc/lms-white/courses/course-creating-with-generate-premium-spark/

Molecular modeling and drug design is a field of study involving computational methods and technologies to identify and develop new drugs that can be used to treat various diseases. This course can provide several benefits to students, including:

– An in-depth understanding of molecular modeling and drug design principles and techniques, which can be helpful in various fields, including pharmaceutical research and development, biotechnology, and academic research.

– Exposure to cutting-edge computational tools and techniques that can predict the structures and functions of proteins and small molecules and evaluate their potential as drug candidates.

– An opportunity to conduct original research that contributes to molecular modeling and drug design and develop the skills and knowledge needed to pursue a career in this field.

– The ability to apply computational approaches to solve real-world biological problems and gain insights into diseases’ molecular basis and the mechanisms of drug action.

Overall, this course can provide students with a comprehensive understanding of the principles and applications of this field and can equip them with the skills and knowledge needed to pursue a successful career in this exciting and rapidly-growing area of science.

Module – I (2 months) Ligand based drug design (Pharmacophore design)
Topics -Introduction and Background
-Understanding different file formats (sdf,mol2,pdb)
-SMILES/canSMILE
-Collection of primary key data
-Pharmacophore preparation
-Chemical Library preparation based on Pharmacophore
-Insilico Screening (ADME)
-Toxicity screening
– QSAR(Quantitative structure-activity relationship) Databases – Pubchem, Drugbank, ZincPharmar etc
-Tools – OpenBabel, Discovery Studio, KNIME, Marvin Sketch, and others (suggestions) etc
Module – II (4 months) Structure based drug design (target-ligand docking)
Topics – Introduction to drug designing
– Data mining, literature study and acquisition of target structure Databases- NCBI, PDB, RCSB, UNIPROT, Modbase
– Comparative modeling of protein (Homology modeling) *target structure not available
– Server based –PHYRE, RaptorX, SWISSMODEL, I-TASSER etc
– Software based–Modeller(standalone)
– Protein structure validation
– Ramachandran plot assessment –RAMPAGE,Pdbsum , Procheck and Profiles3d
– Molecular Docking (AutoDockTools)(file to file command explanation)
– Active site Pocket identification -MetaPocket, CastP etc
– Protein and ligand preparation
– Setting grid parameters and Docking parameters
-Setting up docking on command line
-Docking analysis (based on binding energy, Hydrogen bonds, electrostatic interaction, hydrophobic interaction etc)
-ADT (*Auto Dock vina for multiple ligands)
-BINANA (BINding ANAlyser)
– Pdbsum
Building protein-ligand complex and visualization

Who can apply for Training?

B.Tech. in (Biotechnology/ Industrial Biotechnology/ Bioinformatics/Material Sciences/Computer Sciences)

M.Sc. in (Biotechnology/Microbiology/Chemistry/Biochemistry/Bioinformatics/Life sciences/Material Sciences)

M.Tech. in (Biotechnology/Bioinformatics/ Industrial Biotechnology/Computer Sciences)

B. Pharmacy/M.Pharmacy

]]> 882 Protein Modeling and Molecular Dynamics Simulations https://new.stemskillslab.com/courses/protein-modeling-and-molecular-dynamics-simulations/ Tue, 08 Feb 2022 11:31:12 +0000 http://lmsdemo.loc/lms-white/courses/bio-generate-premium-and-spark-enterprise/

The Protein Modeling and Simulations course offers hands-on training in a specific research area. Students will learn about the structural features and stability of protein structures, as well as model mutations using single and multiple amino acid substitutions. The effects of these mutations on protein structure will be studied using state-of-the-art Molecular Dynamics simulations. Additionally, the course covers the interaction of target proteins with specific ligand molecules, such as inhibitors or activators. Overall, this course provides a comprehensive understanding of protein structure and function through simulations and analysis.

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