Practical Protein Bioinformatics

This Book Describes More Than 60 Web-accessible Computational Tools For Protein Analysis And Is Totally Practical, With Detailed Explanations On How To Use These Tools And Interpret Their Results And Minimal Mentions To Their Theoretical Basis (only When That Is Required For Making A Better Use Of Them). It Covers A Wide Range Of Tools For Dealing With Different Aspects Of Proteins, From Their Sequences, To Their Three-dimensional Structures, And The Biological Networks They Are Immersed In. The Selection Of Tools Is Based On The Experience Of The Authors That Lead A Protein Bioinformatics Facility In A Large Research Centre, With The Additional Constraint That The Tools Should Be Accessible Through Standard Web Browsers Without Requiring The Local Installation Of Specific Software, Command-line Tools, Etc. The Web Tools Covered Include Those Aimed To Retrieve Protein Information, Look For Similar Proteins, Generate Pair-wise And Multiple Sequence Alignments Of Protein Sequences, Work With Protein Domains And Motifs, Study The Phylogeny Of A Family Of Proteins, Retrieve, Manipulate And Visualize Protein Three-dimensional Structures, Predict Protein Structural Features As Well As Whole Three-dimensional Structures, Extract Biological Information From Protein Structures, Summarize Large Protein Sets, Study Protein Interaction And Metabolic Networks, Etc. The Book Is Associated To A Dynamic Web Site That Will Reflect Changes In The Web Addresses Of The Tools, Updates Of These, Etc. It Also Contains Qr Codes That Can Be Scanned With Any Device To Direct Its Browser To The Tool Web Site. This Monograph Will Be Most Valuable For Researchers In Experimental Labs Without Specific Knowledge On Bioinformatics Or Computing. Sequences -- Structures -- Systems. By Florencio Pazos, Mónica Chagoyen. Introduction 5 Contents 7 Chapter-1 9 Sequences 9 1.1 Introduction 9 1.2 Representing Protein Sequences in the Computer 9 1.2.1 Sequence File Formats 10 FASTA Format 10 1.2.2 Sequence Format Conversion Tools 11 1.3 Main Protein Sequence Databases 11 1.3.1 Sequences and Database Entries 13 The Annotations 14 Searching the UniProt 15 1.4 Basic Sequence-Based Characteristics 17 1.5 Compare Two Protein Sequences 18 1.5.1 Types of Pair-Wise Sequence Alignments 20 1.6 Finding Similar Sequences in a Database (Basic) 22 1.6.1 Which Sequence Database to Search? 23 1.6.2 BLAST 23 Interpreting BLAST’s Output 25 1.7 Compare More than Two Sequences 28 1.7.1 Multiple Sequence Alignments: Formats and Conversion 31 1.7.2 Alignment Editing and Representation 31 1.7.3 Summarizing MSAs 34 Consensus Sequence 34 Sequence Logos 35 1.8 Finding Similar Sequences in a Database (Advanced) 37 1.8.1 Sequence Profiles 37 1.8.2 Iterative Profile Construction 38 1.8.3 HMM Profile Search Against a Sequence Database 39 1.8.4 HMM Profile Search Against a Profile Database 39 1.9 Protein Motifs, Domains and Families 40 1.10 Basic Phylogeny 44 Chapter-2 50 Structures 50 2.1 Introduction 50 2.1.1 Storing Protein Structures—The PDB File Format 50 2.2 Main Protein Structure Databases 52 2.2.1 Classifications of Structural Domains 56 2.3 Structure Manipulation, Visualization and Comparison 59 2.3.1 Structure Manipulation and Visualization 59 2.3.2 Structure Comparison 62 Pair-Wise Structural Alignment (Comparing Two Structures) 62 Looking for Structural Homologues (Finding Similar Structures in a Database) 64 Multiple Structural Alignments (Comparing More than Two Structures) 67 2.4 Prediction of 1D Structural Features 68 2.4.1 Secondary Structure and Solvent Accessibility 68 2.4.2 Transmembrane Segments 70 2.4.3 Coiled-Coils 73 2.4.4 Disordered Regions 75 2.4.5 Protein Sorting Signals 78 2.5 Predicting Protein 3D Structure 79 2.5.1 Template-Based (Homology-Based Approaches) 81 2.5.2 Template-Based (Fragment-Based Approaches) 83 2.5.3 Model Quality Checks 84 2.6 Analysis of Protein Structure 85 2.6.1 Mapping Conservation 85 2.6.2 Protein and Ligand Contacts 86 2.6.3 Surface Clefts, Binding Pockets, Tunnels and Internal Cavities 88 Chapter-3 91 Systems 91 3.1 Introduction 91 3.1.1 Protein/Gene Functional Annotations 91 3.1.2 ID Conversions 93 3.2 Annotation Enrichment Analysis of Large Proteins Sets 93 3.3 Protein Interaction Networks 96 3.4 Metabolic Networks 98 3.4.1 Retrieve the Metabolic-Related Information Associated to a Protein of Interest 98 3.4.2 Map a Large Set of Proteins in the Metabolome 101 3.5 Other Biological Networks 103 Bibliography 106 Index 110 Front Matter....Pages i-viii Sequences....Pages 1-41 Structures....Pages 43-83 Systems....Pages 85-99 Back Matter....Pages 101-106