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BIF401 177 Structure Visualization – II (V-U)
- Course:Bioinformatics I (V-U)
- Discipline:Basic and Health Sciences
- Institute:Virtual University
- Instructor(s): Dr. Safee Ullah Choudhry
- Level:Undergraduate
Bioinformatics I (V-U)
- BIF401 001 Background of bioinformatics (V-U)
- BIF401 002 Introduction to bioinformatics (V-U)
- BIF401 003 Need for Bioinformatics – I (V-U)
- BIF401 005 Applications of Bioinformatics – I (V-U)
- BIF401 004 Need for Bioinformatics – II (V-U)
- BIF401 006 Applications of Bioinformatics – II (V-U)
- BIF401 007 Frontiers in Bioinformatics – I (V-U)
- BIF401 008 Frontiers in Bioinformatics – II (V-U)
- BIF401 010 Overview of Course Contents – II (V-U)
- BIF401 009 Overview of Course Contents – I (V-U)
- BIF401 011 Overview of Course Contents – III (V-U)
- BIF401 012 Gene, mRNA and Protein Sequences (V-U)
- BIF401 013 Transcription (V-U)
- BIF401 015 Translation (V-U)
- BIF401 014 Nucleotides (V-U)
- BIF401 016 Amino Acids (V-U)
- BIF401 017 Storage of Biological Sequence Information (V-U)
- BIF401 018 Using Entrez (V-U)
- BIF401 019 Using Uniprot (V-U)
- BIF401 021 Similarities and Differences in Sequences (V-U)
- BIF401 020 Comparing Sequences (V-U)
- BIF401 022 Pairwise Sequence Alignment-I (V-U)
- BIF401 023 Pairwise Sequence Alignment-II (V-U)
- BIF401 025 Dot Plots (V-U)
- BIF401 024 Pairwise Sequence Alignment-III (V-U)
- BIF401 026 Example of Dot Plots (V-U)
- BIF401 027 Identity vs. Similarity (V-U)
- BIF401 028 Introduction to Alignment Approaches (V-U)
- BIF401 030 Aligning In-dels (V-U)
- BIF401 029 Why local alignments? (V-U)
- BIF401 031 Aligning Mutations in Sequences (V-U)
- BIF401 032 Introduction to Dynamic Programming (V-U)
- BIF401 034 Dynamic Programming Methodology (V-U)
- BIF401 033 Dynamic Programming – Essentials (V-U)
- BIF401 035 Needleman Wunsh Algorithm-I (V-U)
- BIF401 036 Needleman Wunsh Algorithm-II (V-U)
- BIF401 037 Needleman Wunsh Algorithm-III (V-U)
- BIF401 039 Backtracking Alignments (V-U)
- BIF401 038 Needleman Wunsh Algorithm-Example (V-U)
- BIF401 040 Revisiting Global and Local Alignment (V-U)
- BIF401 041 Overlap Matches (V-U)
- BIF401 042 Example of Overlap Matches (V-U)
- BIF401 043 Moving From global to local alignment (V-U)
- BIF401 045 Example of Smith Waterman Algorithm (V-U)
- BIF401 044 Smith Waterman Algorithm (V-U)
- BIF401 046 Repeated Alignments (V-U)
- BIF401 047 Exmaple of repeated alignment (V-U)
- BIF401 049 Introduction to Scoring Alignments (V-U)
- BIF401 048 Review of Traceback Strategies for … (V-U)
- BIF401 050 Measuring alignments by scoring (V-U)
- BIF401 051 Scoring matrices (V-U)
- BIF401 052 Deriving scoring matrices (V-U)
- BIF401 053 PAM Matrices (V-U)
- BIF401 054 BLOSSUM Matrices (V-U)
- BIF401 055 Introduction to Multiple Sequences Alignment (V-U)
- BIF401 057 Progressive Alignment for MSA (V-U)
- BIF401 056 More on Multiple Sequence Alignment (V-U)
- BIF401 058 MSA Example (V-U)
- BIF401 059 CLUSTAL (V-U)
- BIF401 061 Introduction to BLAST – II (V-U)
- BIF401 060 Introduction to BLAST – I (V-U)
- BIF401 062 BLAST Algorithm (V-U)
- BIF401 063 Types of BLAST (V-U)
- BIF401 064 Summary of BLAST (V-U)
- BIF401 065 Introduction to FastA-I (V-U)
- BIF401 067 FASTA Algorithm (V-U)
- BIF401 066 Introduction to FastA-II (V-U)
- BIF401 068 Types of FASTA (V-U)
- BIF401 069 Summary of FASTA (V-U)
- BIF401 071 Expasy (V-U)
- BIF401 070 Biological Databases and Online Tools (V-U)
- BIF401 072 Uniprot, SwissProt (V-U)
- BIF401 073 Protein Data Bank (V-U)
- BIF401 074 Review of Sequence Alignment (V-U)
- BIF401 075 GenBank (V-U)
- BIF401 076 Molecular evolution and phylogeny (V-U)
- BIF401 077 Evolution of sequences (V-U)
- BIF401 078 Concepts and Terminologies – I (V-U)
- BIF401 079 Concepts and Terminologies – II (V-U)
- BIF401 080 Algorithm and Techniques (V-U)
- BIF401 081 Introduction to UPGMA (V-U)
- BIF401 082 UPGMA-I (V-U)
- BIF401 083 UPGMA-II (V-U)
- BIF401 084 UPGMA-III (V-U)
- BIF401 085 UPGMA-IV (V-U)
- BIF401 086 UPGMA-V (V-U)
- BIF401 087 DNA to RNA Sequences, Base Compleme… (V-U)
- BIF401 089 Significance of RNA Structures (V-U)
- BIF401 088 Types of RNA and their Function (V-U)
- BIF401 090 RNA Folding, Energies of Folding (V-U)
- BIF401 091 Calculating Energies of Folding – A… (V-U)
- BIF401 092 Types of RNA Secondary Structures I (V-U)
- BIF401 093 Types of RNA Secondary Structures -II (V-U)
- BIF401 095 RNA Tertiary Structures (V-U)
- BIF401 094 Types of RNA Secondary Structures -III (V-U)
- BIF401 096 Circular Representation of RNA Structures (V-U)
- BIF401 097 Experimental Methods for Determination (V-U)
- BIF401 098 Strategies for RNA Structure Prediction (V-U)
- BIF401 099 Dot Plots for RNA 2' Structure Pred… (V-U)
- BIF401 100 Energy Based Methods (V-U)
- BIF401 101 Zuker Algorithm (V-U)
- BIF401 102 Example – Zuker Algorithm (V-U)
- BIF401 103 Zuker Algorithm – Flowchart (V-U)
- BIF401 104 Martinez Algorithm (V-U)
- BIF401 106 Nussinov -Jacobson Algorithm Overview (V-U)
- BIF401 105 Dynamic Programming Approaches (V-U)
- BIF401 107 NJ Algorithm Flowchart (V-U)
- BIF401 108 Example – Jacobson Algorithm (V-U)
- BIF401 109 Score Calculations and Traceback (V-U)
- BIF401 111 Web Resources: RNA Bricks (V-U)
- BIF401 110 Comparison of Algorithms (V-U)
- BIF401 112 Web resources: MFOLD (V-U)
- BIF401 113 From DNA/RNA Sequences to Proteins (V-U)
- BIF401 115 Open Reading Frames (V-U)
- BIF401 114 Coding of Amino Acids (V-U)
- BIF401 116 ORF Extraction – A Flowchart (V-U)
- BIF401 117 Sequencing Proteins (V-U)
- BIF401 118 Application of MS in sequencing (V-U)
- BIF401 119 Techniques for MS Proteomics (V-U)
- BIF401 120 Types of MS-based proteomics (V-U)
- BIF401 122 Two Approaches for Bottom Up Proteome (V-U)
- BIF401 121 Bottom Up Proteomics (V-U)
- BIF401 123 Top Down Proteomics (V-U)
- BIF401 124 Protein Identification (V-U)
- BIF401 125 Protein Ionization Techniques (V-U)
- BIF401 126 MS1 and Intact Protein Mass (V-U)
- BIF401 127 Scoring Intact Protein Mass (V-U)
- BIF401 128 Protein Fragmentation Techniques (V-U)
- BIF401 129 Tandem MS (V-U)
- BIF401 131 Calculating Theoretical Fragment's Mass (V-U)
- BIF401 130 Measuring Experimental Fragment's M… (V-U)
- BIF401 132 Peptide Sequence Tags (V-U)
- BIF401 133 Extracting Peptide Sequence Tags (V-U)
- BIF401 134 Using Peptide Sequence Tags in Protein (V-U)
- BIF401 135 Scoring Peptide Sequence Tags (V-U)
- BIF401 136 In silico Protein Fragmentation (V-U)
- BIF401 137 In silico Fragment Comparison and Scoring (V-U)
- BIF401 138 Protein Sequence Database Search Algorithm (V-U)
- BIF401 139 Integrative Scoring Schemes (V-U)
- BIF401 140 Large Scale Proteomics (V-U)
- BIF401 141 Proteomics Data File Formats (V-U)
- BIF401 143 MGF File Format (V-U)
- BIF401 142 RAW File Format (V-U)
- BIF401 144 Open MS Data Formats (V-U)
- BIF401 145 Online Proteomics Tools – Mascot (V-U)
- BIF401 146 Online Proteomics Tools – ProSight … (V-U)
- BIF401 148 Example Case Study – II (V-U)
- BIF401 147 Example Case Study – I (V-U)
- BIF401 149 Example Case Study – III (V-U)
- BIF401 150 Example Case Study – IV (V-U)
- BIF401 151 Example Case Study – V (V-U)
- BIF401 152 Example Case Study – VI (V-U)
- BIF401 153 Properties of Amino Acids – I (V-U)
- BIF401 155 Properties of Amino Acids – III (V-U)
- BIF401 154 Properties of Amino Acids – II (V-U)
- BIF401 156 Properties of Amino Acids – IV (V-U)
- BIF401 157 Properties of Amino Acids – V (V-U)
- BIF401 158 Structural Traits of Amino Acids – VI (V-U)
- BIF401 159 Structural Traits of Amino Acids – VII (V-U)
- BIF401 161 Structural Traits of Amino Acids – IX (V-U)
- BIF401 160 Structural Traits of Amino Acids – VIII (V-U)
- BIF401 162 Introduction to Protein Folding (V-U)
- BIF401 163 Importance of Protein Folding (V-U)
- BIF401 164 Computing Protein Folding Possibilities (V-U)
- BIF401 166 Models of Protein Folding (V-U)
- BIF401 165 Process of Protein Folding (V-U)
- BIF401 167 Protein Structures (V-U)
- BIF401 168 Primary, Secondary, Tertiary and Quaterly (V-U)
- BIF401 169 Primary Structure of Proteins (V-U)
- BIF401 171 Secondary Structures of Proteins -II (V-U)
- BIF401 170 Secondary Structures of Proteins – I (V-U)
- BIF401 172 Tertiary Structures of Proteins (V-U)
- BIF401 173 Quaternary Structures of Proteins (V-U)
- BIF401 174 Introduction to Protein Bond Angles (V-U)
- BIF401 175 Ramachandran Plot (V-U)
- BIF401 176 Structure Visualization – I (V-U)
- BIF401 177 Structure Visualization – II (V-U)
- BIF401 178 Experimental Determination of Protein (V-U)
- BIF401 179 Protein Data Bank 2 (V-U)
- BIF401 180 Visualization Techniques (V-U)
- BIF401 182 Types of Protein Visualizations (V-U)
- BIF401 181 Online Resources for Protein Visualizations (V-U)
- BIF401 183 Introduction to Energy of Protein Structure (V-U)
- BIF401 184 Calculating Energies of Protein Structure (V-U)
- BIF401 185 Structure Determination for Energy … (V-U)
- BIF401 187 Protein Structures – Alpha Helices I (V-U)
- BIF401 186 Review of Experimental Structure Determination (V-U)
- BIF401 188 Protein Structures – Alpha Helices II (V-U)
- BIF401 189 Protein Structures – Beta Sheets I (V-U)
- BIF401 190 Protein Structures – Beta Sheets II (V-U)
- BIF401 191 Protein Structures – Loops I (V-U)
- BIF401 192 Protein Structures – Loops II (V-U)
- BIF401 193 Protein Structures – Coils (V-U)
- BIF401 195 Structure Classification – II (V-U)
- BIF401 194 Structure Classification – I (V-U)
- BIF401 196 Examples of Protein Domains (V-U)
- BIF401 197 CATH Classification (V-U)
- BIF401 198 Classification Databases (V-U)
- BIF401 199 Algorithms for Structure Classification (V-U)
- BIF401 200 Protein Structure Comparison (V-U)
- BIF401 201 Strategies for Structure Comparison I (V-U)
- BIF401 202 Strategies for Structure Comparison II (V-U)
- BIF401 203 Online Resources for Structure Comparison (V-U)
- BIF401 204 Protein Structure Prediction (V-U)
- BIF401 206 Introduction to Chou Fasman Algorithm (V-U)
- BIF401 205 Predicting Secondary Structures (V-U)
- BIF401 207 2’ Structures in Chou Fasman Algorithm (V-U)
- BIF401 208 Chou Fasman Algorithm – I (V-U)
- BIF401 209 Chou Fasman Algorithm – II (V-U)
- BIF401 210 Chou Fasman Algorithm – III (V-U)
- BIF401 211 Chou Fasman Algorithm – IV (V-U)
- BIF401 212 Chou Fasman Algorithm – Flowchart I (V-U)
- BIF401 213 Chou Fasman Algorithm – Flowchart II (V-U)
- BIF401 215 Chou Fasman Algorithm – Improvement… (V-U)
- BIF401 214 Chou Fasman Algorithm – Flowchart III (V-U)
- BIF401 216 Summary of Visualization, Classification (V-U)
- BIF401 217 Introduction to Homology modelling (V-U)
- BIF401 218 Homology, Paralogy and Orthology (V-U)
- BIF401 220 Seven Steps to Homology Modelling -I (V-U)
- BIF401 219 Workflow for Structural Modelling (V-U)
- BIF401 221 Seven Steps to Homology Modelling -II (V-U)
- BIF401 222 Seven Steps to Homology Modelling -III (V-U)
- BIF401 223 Seven Steps to Homology Modelling -IV (V-U)
- BIF401 224 Seven Steps to Homology Modelling -V (V-U)
- BIF401 225 Seven Steps to Homology Modelling -VI (V-U)
- BIF401 226 Modeller for Homology Modelling (V-U)
- BIF401 227 Online Tools for Fold Recognition (V-U)
- BIF401 228 iTASSER (V-U)
- BIF401 229 GOR Algorithm (V-U)
- BIF401 230 Online Tools for Threading – iTasse… (V-U)
- BIF401 232 Machine Learning Approaches to Structure (V-U)
- BIF401 231 Advantages and Disadvantages of Thr… (V-U)
- BIF401 233 Introduction to Ab-Initio Modelling (V-U)
- BIF401 234 Rationale of Ab Initio Modelling (V-U)
- BIF401 235 Strategies for Ab Initio Modelling (V-U)
- BIF401 236 Energy States of Folded Proteins (V-U)
- BIF401 238 Pros and Cons of Ab Initio Modelling (V-U)
- BIF401 237 Local versus Global Minima (V-U)
- BIF401 239 Summary of Structural Modelling – I (V-U)
- BIF401 240 Summary of Structural Modelling – II (V-U)
- BIF401 241 Summary of Structural Modelling – III (V-U)
- BIF401 242 Review of Sequence Analysis (V-U)
- BIF401 243 Review of Phylogenetics (V-U)
- BIF401 244 Review of Protein Sequencing (V-U)
- BIF401 246 Review of Protein Structures (V-U)
- BIF401 245 Review of RNA Structure Prediction (V-U)
- BIF401 247 Review of Homology Modelling (V-U)
- BIF401 248 Conclusions from this Course (V-U)
- BIF401 249 Advanced Follow-up Courses (V-U)
- BIF401 250 Careers in Bioinformatics (V-U)