Bioinformatics : A Primer

The central aims are: elucidation (by experimental methods) of structural features of the biological entities (proteins, nucleic acids, etc.), application of computational tools and approaches to study of information content, organization, and processing in biological systems, application of medical and health data at the molecular level (biomedinformatics), annotation of structural and chemical characteristics in molecular and drug design (cheminformatics). Thus, it requires trans-disciplinary collaboration between biophysicists, drug chemists, molecular biologists, biomedical and computer-aided modeling experts. Acquisition of high-throughput biological data (e.g. from the genomic projects) at fast rate has ushered in computer-intensive data analysis (in silico analysis). But, considerable 'algorithmic' complexity of biological systems requires a vast of amount of detailed information (experimental and computational) at the cellular and molecular levels for their complete description. Therefore, there is a need for books in this subject with due emphasis on both experimental as well as computational aspects. With these broad objectives in mind, the material contents of this book are organized under-molecular biophysics, experimental methods of structure elucidation, database search, data mining and analysis, computational methods of structure prediction, and rational molecular/drug design (molecular engineering) and validation, with easy interface between these areas and various chapters. Ample tables and figures are intended to facilitate the readers an insight to the structure-function features at the molecular level. Exercise modules and bibliography for each chapter, and glossary are aimed at providing the reader wider perception and insight to the subject matter, and scientific and technical terms. Index is provided to help an easy access to the words and topics to the subject matter. Medical Sciences, Biological Sciences & Biotechnology Bioinformatics,is,the,bridge,between,experimental,data,in,diverse,biologically,related,disciplines,and,extrapolation,of,information;,by,computational,analysis;,about,how,the,systems,and,processes,function.,The,central,aims,are:,(i),elucidation,(by,experimental,methods),of,structural,features,of,the,biological,entities,(proteins;,nucleic,acids;,etc.);,(ii),application,of,computational,tools,and,approaches,to,study,of,information,content;,organization;,and,processing,in,biological,systems;,(iii),application,of,medical,and,health,data,at,the,molecular,level,(biomedinformatics);,annotation,of,structural,and,chemical,characteristics,in,molecular,and,drug,design,(cheminformatics).,Thus;,it,requires,trans-disciplinary,collaboration,between,biophysicists;,drug,chemists;,molecular,biologists;,biomedical,and,computer-aided,modeling,experts.;,Acquisition,of,high-throughput,biological,data,(e.g.,from,the,genomic,projects),at,fast,rate,has,ushered,in,computer-intensive,data,analysis,(in,silico,analysis).,But;,considerable,"algorithmic",complexity,of,biological,systems,requires,a,vast,of,amount,of,detailed,information,(experimental,and,computational),at,the,cellular,and,molecular,levels,for,their,complete,description.,Therefore;,there,is,a,need,for,books,in,this,subject,with,due,emphasis,on,both,experimental,as,well,as,computational,aspects.;,With,these,broad,objectives,in,mind;,the,material,contents,of,this,book,are,organized,under-molecular,biophysics;,experimental,methods,of,structure,elucidation;,database,search;,data,mining,and,analysis;,computational,methods,of,structure,prediction;,and,rational,molecular/drug,design,(molecular,engineering),and,validation;,with,easy,interface,between,these,areas,and,various,chapters.,Ample,tables,and,figures,are,intended,to,facilitate,the,readers,an,insight,to,the,structure-function,features,at,the,molecular,level.,Exercise,modules,and,bibliography,for,each,chapter;,and,glossary,are,aimed,at,providing,the,reader,wider,perception,and,insight,to,the,subject,matter;,and,scientific,and,technical,terms.,Index,is,provided,to,help,an,easy,access,to,the,words,and,topics,to,the,subject,matter. Bioinformatics is the bridge between experimental data in diverse biologically related disciplines and extrapolation of information,by computational analysis,about how the systems and processes function. The central aims are: (i) elucidation (by experimental methods) of structural features of the biological entities (proteins,nucleic acids,etc.),(ii) application of computational tools and approaches to study of information content,organization,and processing in biological systems,(iii) application of medical and health data at the molecular level (biomedinformatics),annotation of structural and chemical characteristics in molecular and drug design (cheminformatics). Thus,it requires trans-disciplinary collaboration between biophysicists,drug chemists,molecular biologists,biomedical and computer-aided modeling experts.,Acquisition of high-throughput biological data (e.g. from the genomic projects) at fast rate has ushered in computer-intensive data analysis (in silico analysis). But,considerable "algorithmic" complexity of biological systems requires a vast of amount of detailed information (experimental and computational) at the cellular and molecular levels for their complete description. Therefore,there is a need for books in this subject with due emphasis on both experimental as well as computational aspects.,With these broad objectives in mind,the material contents of this book are organized under-molecular biophysics,experimental methods of structure elucidation,database search,data mining and analysis,computational methods of structure prediction,and rational molecular/drug design (molecular engineering) and validation,with easy interface between these areas and various chapters. Ample tables and figures are intended to facilitate the readers an insight to the structure-function features at the molecular level. Exercise modules and bibliography for each chapter,and glossary are aimed at providing the reader wider perception and insight to the subject matter,and scientific and technical terms. Index is provided to help an easy access to the words and topics to the subject matter. Cover......Page 1 Preface......Page 8 Acknowledgement......Page 10 Contents......Page 12 1.1 "Bioinformatics"......Page 14 1.2 The Objectives of Bioinformatics......Page 17 2.1 Atomic Structure......Page 24 2.2 Molecules......Page 26 3.1 Constituents of Nucleic Acids......Page 28 3.2 Polynucleotides......Page 29 3.3 The Genome Projects......Page 34 4.1 Amino Acids......Page 43 4.2 Proteins......Page 47 4.3 Forces Stabilizing the Molecular Structure......Page 55 Chapter 5 Physicochemical Characterization of Biomolecules......Page 64 5.1 Hydrodynamical Methods......Page 65 5.2 Chromatographic Methods......Page 68 5.3 Electrophoretic Methods ......Page 69 5.4 Blotting Techniques......Page 79 6.1 Primary Structure Determination of Nucleic Acids......Page 83 6.2 Primary Structure Determination of Proteins......Page 89 7.1 X-Ray Diffraction Methods......Page 96 7.2 Nuclear Magnetic Resonance (NMR) Spectroscopy......Page 102 7.3 Imaging Methods......Page 108 8.1 Protein-Nucleic Acid Interactions......Page 115 8.4 Protein-Lipid Interactions......Page 123 Chapter 9 The Protein-folding Problem......Page 128 9.1 Genomics Analysis......Page 129 9.2 Proteomic Analysis......Page 138 10.1 Protein Folding Rules......Page 146 10.2 Structure Prediction of Fibrous Proteins......Page 147 10.3 Structure Prediction of Globular Proteins......Page 148 10.4 Application of Structure Prediction Programs......Page 157 11.1 Primary Structure (Sequence)......Page 164 11.2 Databases......Page 165 11.3 Genome Datbase Search......Page 168 11.4 Protein Database Search......Page 173 Chapter 12 Data Mining, Analysis and Modeling......Page 181 12.1 Sequence Alignment Analysis......Page 183 12.2 Pair-Wise Sequence Alignment......Page 186 12.3 Multiple Sequence Alignment (MSA)......Page 191 12.4 Phylogenetic Analysis......Page 197 12.5 Secondary Structure Analysis......Page 203 12.6 Motifs, Domains and Profiles......Page 205 12.8 Protein Classification and Modeling......Page 212 13.1 Disease Gene Identification......Page 225 13.2 Genetic Variations and Genetic Diseases......Page 227 13.3 Genetic Testing and Therapy......Page 229 14.1 Genomics and Proteomics Analysis......Page 236 14.2 Rational Design......Page 240 14.3 Validation......Page 243 Glossary......Page 247 Index......Page 255 About the Book: Bioinformatics is the bridge between experimental data in diverse biologically related disciplines and extrapolation of information, by computational analysis, about how the systems and processes function. The central aims are: (i) elucidation (by experimental methods) of structural features of the biological entities (proteins, nucleic acids, etc.), (ii) application of computational tools and approaches to study of information content, organization, and processing in biological systems, (iii) application of medical and health data at the molecular level (biomedinformatics), a.;Cover; Preface; Acknowledgement; Contents; Chapter 1 Bioinformatics: Introduction; Chapter 2 Atoms and Molecules; Chapter 3 Features of Nucleic Acids; Chapter 4 Features of Proteins; Chapter 5 Physicochemical Characterization of Biomolecules; Chapter 6 Primary Structure (Sequence) Determination of Biomolecules; Chapter 7 Spatial Structure Determination of Biomolecules; Chapter 8 Protein-Ligand Interactions; Chapter 9 The Protein-folding Problem; Chapter 10. Computational Methods in Structure Prediction; Chapter 11 Database Search; Chapter 12 Data Mining, Analysis and Modeling.