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Boolean algebra for informatics –  Flowchart-types of logic used in flowchart-examples.  Hierarchy of programming languages-classification of programming languages-popular programming languages. Characteristics of a good program-program development process-errors in programming.  Introduction to parallel and distributed computing methods.  High performance computing Cloud Computing.    Basic terminology elementary data organization Data structures data structure operation algorithms complexity, time space, trade off.   TREES: Binary trees Algorithm- Representation binary trees in memory – traversing binary trees – traversal algorithms using stacks – Header nodes: Threads – Binary search trees Algorithm– searching and inserting in binary search trees – Deleting in a binary search trees – Heap: Heap sort – General trees.   GRAPHS: Graph theory terminology – Sequential representation of graphs: Adjacency matrix: Path matrix – Warshall’s algorithm: Shortest path – linked representation of a graph – operations on graphs – Traversing a graph – Posets: Topological sorting.  20hrs   Background – The evolution of Programming – the Internet and the worldwide web Java – an overview of Java - Java language basic –Objects, primitive data types – identifiers – keywords- variable – operators and expression – assignment and statement, Classes, Methodical programming – Methods recap – specification – determine the class –Collections – loops –array–sorting – vectors –strings-string buffer, Applets – The Applets Class – methods – inheritance and overriding graphical Programming – Components, AWT, Visual Design – Containers – Layouts – other containers – menus - Events and Actions – event driven programming – AWT event –Event hierarchy – listeners – methods, Introduction to databases – Java Database connectivity -record navigation – Record manipulation, Tools: JDK, IDE Toolkits, Eclipse / Netbeans, JCreator, JDBC Drivers, J.Chem- Case studies. –concept of internet programming and web designing    Introduction to databases – RDBMS, JDBC, Apache Tomcat, JSP/JAVA, MySQL, JCHEM from CHEMAXON, Building web compatible molecular repository a practical approach.   Structured Query Language.- basic, primary key, constraints & triggers, DCL, DML, TCL, DDL, Grant & Revoke permission. Design of Chemical Databases, Data Abstraction; Data Models; Instances & Schemes; E-R Model - Entity and entity sets; Relations and relationship sets; E-R diagrams; Reducing E-R Diagrams to tables; Network Data Model: Basic concepts; Hierarchical Data Model: Basic Concepts; Metadatabases; Indexing and Hashing; Basic concepts; Text Databases; Introduction to Distributed Database Processing, Data Security. Intefacing programs with databases; Structure databases; Reaction Databases; Literature Databases; Medline;GenBank; PIR; CAS Registry; National Cancer Institute (NCI) Database.     Chemical, genomic, proteomics, and literature databases. Sources, contents, design. Accessibility and use  Introduction – Aspects of data mining- data mining models and visualisation – software for chemical data mining – application visualisation system – Data mining and human genome.   History of chemoinformatics, Definition of Chemoinformatics, Chemical Structure representation. Introduction to chemical structure file formats. Linear, 2D and 3D representations. Connection Tables, Molecular structure Searching techniques. Introduction to Molecular Fingerprints. Similarity metrics (Tanimoto Coefficient, Eucledien distance). Computer representation of molecules- Chemical databases -data search –2D and 3D searching. Interconversion of 2D to 3D optimization techniques  10 hrs

 

UNIT II: COMBINATORIAL CHEMISTRY Combinatorial chemistry – Molecular Scaffolds, Design of Scaffolds from library of molecules. Focused virtual library design and analysis. principles and methods. Rule of five, Druglikeliness, Leadlikeliness, Screening, Drug design and combinatorial libraries– case studies.  25hrs UNIT III : DRUG DESIGN AND DISCOVERY Contour of Drugs –-Development of New Drugs – molecular recognition in drug design- Introduction to molecular diversity ; molecular similarity (Tanimoto, Eucledian, Dice, Cosine) – molecular descriptors (1D, 2D, 3D)- partition coefficient (LogP)– molar refractivity-pharmacophore keys- similarity calculation stereochemistry in drug design -Prodrugs and Soft Drugs -Drug Targets -Drug Solubility – Lead optimization Molecular Diversity- natural Resources of lead Compounds –case studies.  25 hrs

 

UNIT IV : DATABASES Chemical database design- Chemical Abstract Service, Pubchem (Compounds, Substances, Bioassay), PubMed, EPA, FDA, RTECTS, NIOSTIC, DrugBank, ChemBank, ChemSpider, ChemExper, SPECS, Commercial Chemical Suppliers Database, NCI, MOLTABLE.  35 hrs REFERENCE BOOKS: 1. Larsen et al (ed), Textbook of drug design and discovery, 3rd edition, Taylor and Francis, London and New York, 2004. 2. Ashutosh Kar, Medicinal Chemistry, III ed, New Age International publishers, New Delhi. CHE 6524M - COMPUTATIONAL CHEMISTRY AND MOLECULAR MODELING  SEMESTER VI LAB CUM THEORY 5 hrs/week UNIT I: COMPUTATIONAL CHEMISTRY Experimental aspects and computer models of molecules and their behavior in gas and condensed phases; quantum and molecular mechanics - Force field and its applications- multiple regression analysis- implicit and explicit solvation models; conformational analysis; energy minimisation; Basic concepts of Ab Initio molecular dynamics and Monte Carlo simulations.  (Theory: 20 hrs; Lab: 15 hrs) Labwork with software like Gaussian, MOPAC, MOE, JCHEM, MarvinSketch, MarvinView, MarvinSpace  UNIT II: MOLECULAR MODELING Ligand based Drug Design, Quantitative structure-activity relationships (QSAR)- Introduction of Molecular Descriptors (1D,2D and 3D), Statistical analysis- Linear and Non linear Methods, PLS, PCA, PCR, ANN, kNN, SVM, Binary methods. Elementary ideas of comparative molecular field analysis (CoMFA). Pharmacophore modeling, structure-based design; docking and scoring functions; Structure based de novo design techniques –Molecular Docking, Active Site characterization, Case study of designing HIV I protease Inhibitor- Quantitative structure-property relationships (QSPR) – Predicting Melting Point, Solubility, Boiling point, TPSA etc.,. Quantitative Structure Toxicity Relationships (QSTR), Aquatic Toxicity, Carcinogenicity, Mutagenicity,  (Theory: 30 hrs; Lab: 30 hrs) Chemical Databases Introduction to publicly available molecular databases, Pubchem, Literature databases (PubMed), Introduction to NCBI web resource. Learning MeSH, NLM Database, NCI Database, DRUGBank, FDA Drugs, EPA Chemical Databases, RTECS etc., Searching and Retrieving molecular data and other physico chemical, biological, toxicological data from web sources for QSAR, QSPR and QSTR related studies.  (Theory: 20 hrs; Lab: 20 hrs)    

 

Referece: Practical Chemoinformatics: M Karthikeyan and Renu Vyas (2014) Springer .(in press) Purchase from Springer Amazon