dear all
following syllabus can be used as a starting point
jaleel
Paper-I Basics of Cheminformatics
UNIT I - Basic Mathematics and
Statistics
Graph theory and
molecular numerology; Logic, sets and functions; Algorithms, integers and
matrices; Mathematical reasoning, induction and recursion; Counting; graphs,
trees and sets, basic probability and
statistics; Markov processes
UNIT II - Foundations of
Chemistry and Biology
Basic Stereochemistry, Group Theory, Amino acids
and Proteins and Properties; pKa, pH and ionization of acids and bases; Protein
structure - Primary structure, Secondary structure - helix & sheet; Tertiary
structure; Quaternary structure; covalent and non-covalent forces that maintain
structures. Physical properties of proteins - charge, size, hydrophobic, protein
binding – structural aspects; antibodies; transport; nucleotide binding;
catalytic enzymes; basic concepts of combinatorial chemistry. Introduction to
drug action, pro drug design and applications
UNIT III - Chemical information
sources
History of scientific information
communication-chemical literature-chemical information-chemical information
search-chemical information sources-chemical name and formula
searching-analytical chemistry-chemical history-biography-directories and
industry sources
UNIT IV - Bioinformatics
Introduction; Experimental sources of biological
data; Publicly available databases; Gene _expression_ monitoring; Genomics and
Proteomics; Metabolomics; Visualisation of sequence data; Visualization of
structures using Rasmol or SPDB Viewer or CHIME;
Genetic basis of disease; Personalised medicine and gene-based
diagnostics; Legal, ethical and commercial ramifications of
bioinformatics
UNIT V - Pharmaceutical applications of
molecular modeling
Introduction to drugs, structure-based drug
design. QSAR and 3D-QSAR Methods. Pharmacophore Design, Ligand-Based Design and
De Novo Drug Design Virtual sreening/docking of ligands. Protein
structure. Drug action enzymes. Drug action receptors. Drug design target
interaction. Prediction of Binding Modes, Protein–ligand binding free
energies, Fragment-Based Drug Design; Absorption, Distribution, Metabolism,
Excretion & Toxicology (ADMET) prediction; Calculation of Physico-Chemical
Properties, Biological and Physico-Chemical Predictive Model
Building
PAPER II Computer Programming and NETWORKING FOR
CHEMINFORMATICS
UNIT-I Operating systems – Human interface, Algorithms-genetic algorithms- neural networks- Artificial intelligence, Grid & high-performance computing, Software, Open source. Document mark up languages: HTML,XHTML, XML: Key terminology, Characters and escaping,Well-formedness and error-handling, Schemas and validation Related specifications, Use on the Internet, Programming interfaces, Chemical Markup Language
UNIT II – Basics of C & C++ : Basic Syntax - Variables, Constants and Built-in Types - Operators and Basic Expressions - Flow Control and Statement Blocks - Functions and Arguments - Modules and Scope – Arrays - Character Strings – Pointers - Defining New Types - Classes and Objects – Casts – Preprocessor The Programming Process - Writing Source Code
UNIT III - JAVA Programming -Introduction to Java - _javascript_ for Cheminformatics: Basic Syntax - Variables, Constants and Built-in Types - Operators and Basic Expressions - Flow Control and Statement Blocks - Functions and Arguments - Modules and Scope – Arrays - Character Strings – Pointers - Defining New Types - Classes and Objects – Casts – Preprocessor The Programming Process - Writing Source Code
UNIT IV - Programming in PERL and PYTHON : PERL: Introduction, Basic operators and control structures, Scalars, Lists, Hashes, File Manipulation, Pattern Matching and Regular Expressions, Subroutines, Text and string Processing Python Programming: Overview-Data structures-control flow-modules-basic I/O, Exception Handling, Regular expressions, File manipulation, classes, standard library
UNIT V - Computer networking: Introduction Network classification: Connection method- Scale- Functional relationship (network architecture)-Network topology Types of networks: Personal area network-Local area network-Campus area network- Metropolitan area network-Wide area network- Global area network- Virtual private network Internetwork: Intranet- Extranet-Internet Basic hardware components: Network interface cards, Repeaters, Hubs,Bridges,Switches, Routers
Paper –III CHEMINFORMATICS DATABASE design and their management
UNIT I - Database Concepts: Relational Databases-Object Databases-Basic SQL- Data types- Operators Advanced Queries: Joins, Built-in Functions, Improving Query Performance, Group by,Stored Procedures Views, Catalogs and Integrity: Creating tables- Verifying Integrity- Creating Views- Database Catalog E-R Model and Normalization - Entity and entity sets; Relations and relationship sets; E-R diagrams; Reducing E-R Diagrams to tables; Security, Backup and Recovery: Creating users- Encrypting traffic- Backup of the database- Recovery
Popular Databases and differences: Oracle- SQL Server- DB2
Unit II - Network Data Model: Basic concepts; Hierarchical Data Model: Basic Concepts; Multimedia Databases - Basic Concepts and Applications; Indexing and Hashing; Basic concepts (ISAM, B+ Tree indexed files, B Tree indexed files, Static Hash functions, Dynamic Hash functions); Text Databases; Introduction to Distributed Database Processing, Data Security. Interfacing programs with databases; Data interoperability using XML.
UNIT III - Database Design: Introduction to Schema Refinement- Functional Dependencies-Normal Forms-First , Second, Third, Boyce code, Fourth and Fifth Normal forms- Multivalued Dependencies.
UNIT IV - chemical
databasesIntroduction-chemical databases- types-
chemical database design-Bio Catalysis Database. The MOS Database, reaction
databases, The Failed Reaction Database. Protecting groups database-solid-phase
synthesis database- Sequence Databases, Spectra. Databases, (Bio) Activity/Prop.
Databases, Toxicology Databases.
Unit V - High Throughput Data Processing and Data Mining
Introduction; Data visualization, Non-linear
mapping
Data mining methods, Substructural analysis,
Discriminant Analysis, Neural networks, Decision Trees; Software for Chemical
Data Mining. Data Mining and human genome.
Combinatorial Chemistry Technologies and
Libraries. Chemistry Libraries: Design of Focused, Diverse and Thematic
Libraries. Biological Libraries, Bio planning, Peptide Display Libraries design
and construction.
Paper IV - Computational chemistry
UNIT I - Introduction to computational chemistry -Force fields and molecular representations of matter Intramolecular (bonding) interactions-Non-bonded interactions -Hydrogen bonds-Constraints and Restraints-United atom and other coarse-grained approaches-Non-pairwise interactionsMethods for Simulating Large systems:Non-bonded Cutoffs Shifted potential and shifted force-Switching functions-Neighbor listsBoundaries -Periodic Boundary conditions-Stochastic forces at spherical boundaryLong-range interactions -The Ewald Sum-The Reaction field method
UNIT II - Energy Minimization and related analysis techniques Steepest descent-Conjugate gradient-Newton-Raphson-Comparison of methods-Advanced techniques: Simulated Annealing, Branch-and-bound, simplex-What's the big deal about the minimum anyway? Free Energy :Perturbation methods,Thermodynamic integration
UNIT III - Introduction to Equilibrium Statistical Mechanics Phase space, ergodicity, and Liouville's theorem-Ensemble theory, thermodynamic averages -Statistical mechanics of fluids Monte Carlo -MC integration and Markov chains:The Metropolis method,Biased MC Molecular Dynamics Classical mechanics: equations of motion,Finite Difference methods :Verlet algorithm,Velocity verlet,The Time step: practical issues,Multiple time-step algorithms-Constraint Dynamics :Fundamental concepts ,SHAKE and RATTLE Brownian dynamics and the Langevin Equation
UNIT IV - Temperature: Maxwell-Boltzmann distribution of velocities Temperature control Velocity scaling,Andersen's method,Nose-Hoover dynamics Calculating properties from MD trajectories, Hybrid MC
UNIT V - Chemometrics -Introduction- Origins-Techniques : Multivariate
calibration,Classification, pattern recognition, clustering,Multivariate Curve resolution,Other
Techniques, Commercial Softwares
References:
Paper-V STRUCTURAL BIOLOGY
UNIT I - Introduction to protein structure: Physical and chemical properties of amino acids and polypeptides. Conformational properties of proteins, Ramachandarn Plot, Secondary, Super Secondary, tertiary and quaternary structure of proteins.
UNIT II - Functional classification of proteins: Cell surface receptors, GPCR’s, Kinases, Channel proteins, Ubiquitin
UNIT III - Biophysical Techniques: Principles, Process and Applications of Thin layer chromatography, Column chromatography ( ion exchange and affinity only) , HPLC,
UNIT IV - x-ray generation ; its application; unit cell and x-ray ,anomalous scattering; lattices, Bragg’s Law; atomic scattering factor and structure factor; phase problem; intensity data collection and reduction;
UNIT V - Isolation and purification of protein (chromatography, electrophoresis), crystallization (sitting and hanging drop method). Protein structure determination-molecular replacement technique; multiple isomorphous replacement method, synchrotron radiation and its uses; multi wavelength anomalous diffraction method. Calculation of electron density map, interpretation of electron density map. Refinement of the structure. Structure validation methods.
Paper-VI Molecular modeling techniques
UNIT I: Introduction to Molecular Modelling
Introduction to
Molecular Modelling.
What are models used for? Areas of application – Single
molecule calculation, assemblies of molecules. Reaction of the molecules.
Drawbacks of
mechanical models as compared to graphical models. Co-ordinate systems two
–
matrix,
potential energy surface.
UNIT II – Quantum Mechanics
Postulates of
quantum mechanics,
electronic structure calculations, ab initio, semi-empirical
and density functional theory calculations, molecular size versus accuracy.
Approximate
molecular orbital theories.
UNIT III – Comparative protein modeling
Modelling by
Homology-the alignment,
construction of frame work, selecting variable regions,
side chain placement and refinement, validation of protein models
–Ramchandran
plot,
threading and ab initio modeling.
PAPER VII - PHARMACEUTICAL CHEMISTRY
UNIT I - Molecular basis of drug action: Receptor: Drug Receptor Interaction: Basic ligand concept, agonist, antagonist, partial agonist, inverse agonist, receptor Theories - Occupancy, Rate & Activation Theories, receptor Binding Assays, determination of B-max and Kd by transforming data with Hill plot and Scatchered plot., above concepts with special reference to Opioid , Histaminergic , Adrenergic and GABA nergic receptors. Enzyme Inhibition – Enzyme, enzyme Kinetics, enzyme Inhibitors - reversible, irreversible, Kcat inhibitors.Transition state analogs, enzyme Inhibitors as drugs - ACE, leukotrienes,Lipoxygenase, Cycloxygenase, Aromatase, Xanthine oxidase, DNA PolymeraseInhibitors, HIV - Protease / Reverse Transcriptase, Integrase and Cytochrome P-450 Inhibitors. Drug binding to nucleic acid -- Antimalarial, anti-cancer, antiviral..
UNIT II- Synthon approach:
Definition of terms - disconnection, synthon, functional group interconversion (FGI), Basic rules in Disconnection, Use of synthon approach in synthesis of compounds: Trimethoprim, erfenadine, lbuprofen, Propanolol, Fentanyl,Ciprofloxacin, Cimetidine, Piroxicam,osiglitazone, Diclofenac, Captopryl, Nifedipine, Losartan.
UNIT III- Combinatorial Chemistry
Introduction, combinatorial approaches, chemical Peptide and small molecule libraries, applications, methodology, combinatorial organic synthesis, assays and screening of combinatorial libraries, i6ntroduction to High Throughputs Screening (HTS)
UNIT IV- Nanochemistry
Physical chemistry related to nanoparticles such as colloids and clusters: different equilibrium structures, quantum effects, conductivity and enhanced catalytic activity compared to the same materials in the macroscopic state.Exploitation of self-assembly and self-organization to design functional structures in 1D, 2D or 3D structures.Role of polymers in lithography resists, as well as self-organization of more complicated polymer architectures such as block copolymers and polymer brushes. Nanomaterials: (Nanoparticles, nanoclusters, quantum dots synthesis): Top-down techniques: photolithography, other optical lithography (EUV, X-Ray, LIL), particle-beam lithographies (e-beam, FIB, shadow mask evaporation), probe lithographies, Bottom-up techniques: self-assembly, self-assembled monolayers, directed assembly, layer-by-layer assembly. Pattern replication techniques: soft lithography, nano imprint lithography. Pattern transfer and enhancement techniques: dry etching, wet etching, pattern growth techniques
UNIT V - Microwave synthesis- fundamentals of microwave synthesis- Microwaves Are Energy- Microwaves Can Interact with Matter- Two Principal Mechanisms for Interaction With Matter- Microwave Heating Differs from Conventional Means: Conventional Heating Methods- Microwave Heating - The Microwave Effect with examples - Single-Mode and Multimode Microwave Cavities
Paper-VIII ANALOG and stucture based drug designing
UNIT I - Drug discovery-Strategies and historical developments - Introduction –conventional strategies to drug discovery-molecular mimetic- first and second generation rational approach-Rational drug design-assessment of drug activity- future prospects-examples of successful applications of CAD
UNIT II - Basic principle of drug design: Introduction-old QSAR-Use of physiochemical descriptors-use of electronic descriptors-use of molecular descriptors-Use of thermodynamic descriptors-use of receptor descriptors-success and limitations of old QSAR
UNIT III Analog based drug design
Developing and using QSAR- Introduction-classical QSA-Freem and Wilson’s method-topliss method-use of statistical methods in QSAR-validation methods-3D QSAR approach-QSAR descriptors3D QSAR-Introduction-Pharmacore identification-binding site modeling of unknown receptor-receptor mapping-structural alignment and superposition-molecular field analysis (MFA)
Unit iv Structure based drug design
3D pharmacophores, De novo Ligand design-introduction-approaches to de novo drug design problem-some current methods for de novo design.3D data base searching and virtual screening,. Sources of data, molecular similarity and similarity searching, prediction of binding energy of ligand-receptor complex-Free energies and salvation-electrostatic and non-electrostatic contribution to free energies combinatorial libraries – generation and utility,
UNIT V- Molecular docking: Introduction Docking approaches: Shape complementarity- Simulation Mechanics of docking - Search algorithm-Scoring function-Applications
PRACTICAL I Computer programming and RDBMS
C++, JAVA, CML, Perl, Perl Mol, Python, Visual Basic, ORACLE
PRACTICAL II
Chemical databases - ChemBank-ChemBioFinder – CSChemoffice - ZINC
Molecular dynamics - GROMACS- NAMD-VEGA ZZ
Structural chemistry - NWChem –GAMESS
Docking - Autodock, DOCK -VEGA- FlexX
JALEEL
MCC
Dear CCLrs,Recently my faculty is considering to offer an undergraduate course on Chemoinformatics, for chemistry students. Though I´ve been working a bit on computational chemistry, I do not feel I have the proper vision to built up a syllabus proposal, or even for giving a reasonable criticism of anyone else proposal.I would really appreciate your opinion on what should be included in a course of such a level?Thanks in advance for your kind reply.Rodolfo Gómez