Bioinformatics Training

This course is future for all the professionals who want to understand the basics of Bioinformatics and its applications for furthering their career. Cheminformatics and Bioinformatics training in India have profound demand because of high promise in R&D ahead. This Program aims to provide hands-on experience in Biological databases, Genomics tools, Proteomics tools, visualizing tools, molecular modeling, ligand screening, docking and its techniques, ADMET prediction and Computer Aided Drug Designing (CADD).

Topics covered in the courses are

Basics course of Cheminformatics

Bioinformatics-an Overview, Definition and History Information Networks Internet in Bioinformatics. Classification of amino Acids, Classification and three Dimensional structures of proteins. Overview of protein structure, Ramachandran Plot, Protein purification, Post translation modification, Protein trafficking.
Chemical structure representations : ChemDraw, MarvinSketch, ACD/ChemSketch, jsMol Editor, Marvin molecule editor and viewer, Ketcher, UCSFChimera, Pymol, OpenStructure, OpenBabel, PoseView, Ligplot+
DATABASES: Protein Information Resources- Biological Databases, Primary Sequence databases, GSDB (Genome Sequence Database), Secondary Databases Genome Information Resources- DNA sequence Databases - EMBL, DDBJ, Genbank.
Tools-- Uniprot, NCBI, Zinc database,Prosite, Prints, Blocks, Profiles and Identity. Protein Data bank (PDB), Nucleic Acid Data Bank (NDB), Molecular modeling Data Bank (MMDB), Uniprot, Prosite, SCOP, CATH, KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, Prodom.
Gene prediction and functional analysis. Primer designing, ESTs and Gene discovery, Restriction site detection. Tools-- Open Reading Frame Finder, StarORF, Translator, Translate, Virtual Ribosome, Back Translation, CodonW, Primer3, Webcutter, NEBcutter.
Matrix. Fold recognition. Sequence analysis: pairewise sequence comparison- sequence queries against biological databases- BLAST and FASTA multifunctional tools for analysis. Pair wise sequence alignment, gaps, gap- penalties, scoring matrices, PAM250, BLOSUM62, local and global sequence alignment, multiple sequence alignment, Tools -- BLAST, FASTA, ClusatlW
DNA, RNA Secondary structure predictions. Propensity value. Tools--JPred, PSIPRED, GOR, CentroidFold, IPknot, Mfold, RNAfold
PROTEIN STRUCTURE PREDICTION: Homology modeling and Threading. Prediction of protein structure from sequences, functional sites. Tools--Modelar, I-TASSER, Phyre2, Swissmodel, PepSea, PepMAPPER, FindPept.
Binding site analysis, Model evaluation, and Model validation. CASTp TRAPP, CAVER, sc-PDB, Pocketome, 3DLigandSite, metaPocket, PockDrug
PHYLOGENETIC ANALYSIS : Evolution, elements of phylogeny, methods of phylogenetic analysis, Phylogenetic tree of life, comparison of genetic sequence of organisms, phylogenetic analysis tools- MEGA, Phylip, ClustalW
Genetic algorithm, Algorithms in Bioinformatics
Docking of small molecules. Autodock vina, Igemdock, HDock

Advanced cheminformatics

Molecular Modeling : Introduction, force field, quantum chemistry, Schrödinger equation, potential energy functions, energy minimization, local and global minima, saddle point, grid search, , various approximations; LCAO, HF, semi-empirical calculations; single point calculations, full-geometry optimization methods, ZDO, MNDO, CNDO, NDDO, AM1, PM3, , conformational search, Z-matrix, Energy minimisation, molecular modeling packages. CharmM, Amber etc.tools
Molecular Dynamics, Introduction, Newton’s equation of motion, equilibrium point, radial distribution function, pair correlation functions introduction semi- empritical, Molecular MECHANICS and ab intio techniques Simulation techniques potential energy surfaces
Pharmacophoric pattern : Structure based PharmacoPhore generations, Ligand based PharmacoPhore generations; Tools: Pharmagist Pharmer, Catalyst, PharmaGist, SwissSimilarity, Blaster, AnchorQuery
ADME Properties; QikProp. GastroPlus, VolSurf. ADMEWORKS ModelBuilder, ADMEWORKS Predictor.
Quantitative structure activity relationship Use of genetic algorithms and principle component analysis in the QSAR equations
Drug Discovery and Computer Aided Drug Designing : Introduction, drug discovery area, pharmacogenetics and pharmacogenomics applications, SNPs, parameters in drug discovery identification of drug target molecules, drug design and its approaches, ligand design methods, docking programs; De novo design
Recent advances drug design methodologies, Biomolecular structure, Structure activity relationship, structure-based drug design
Virtual screening. Structure based pharmacophore. Screening of various chemical databases (Ex-Zinc database)

Basics course of Bioinformatics

Syllabus of Basics course of cheminformatics syllabus
Algorithms
Biopython
UNIX

Advanced Bioinformatics

Syllabus of Advanced course of Cheminformatics
Basic course of Bioinformatics
R programming

Immunoinformatics

Syllabus of basics course chemininformatics
Introduction to Immunoinformatics and Immunological Databases- dbMHC-MHC database at NCBI, T-cell epitope databases, B-cell epitope databases. SYFPEITHI MHC-presented epitopes. Tools-- Variosite, Pep-3D
Homology modeling of antibody. Tools--RosettaAntibody, PIGS, WAM
Prediction of Cytotoxic T Cell (MHC Class I) Epitopes- Antigen Processing in the MHC ClassI Pathway. Tools--NetCTL, SYFPEITHI, CTLPred, NetMHC server
MHC-II PREDICTION: Prediction of Helper T Cell (MHC Class II) Epitopes- Processing of MHC Class II Epitopes. Tools--PEPVAC, SVRMHC,NetCTL, BIMAS
BCELLEPITOPE PREDICTION AND WEB SOURCES --Recognition of Antigen by B Cells- vaccine design- Web-Based Tools for Vaccine Design. Tools-- Conservatrix, EpiMatrix, Epi-Assembler, VaccineCAD, EpiMatrix, EpiVax

Faculty:

Well experienced faculty (more than 10yeras experience) from various universities

Eligibility:

UG/PG/PhD students, faculty, scientists in the field of Biotechnology, Life Sciences, Medical Sciences, Pharmaceutical Sciences, Chemical Sciences and related subject areas. Industry professionals who are involved in research and development or interested in acquiring themselves with research are also eligible.

Sailent features:

We provide an individually cared hands-on practical training
Teaching with commercial software
Guest faculties from reputed universities/organization will be arranged
Limited students in each batch
Online classes, Weekend classes.
Placement assistance for worthy candidates

CIENCIA LIFE SCIENCES