BIOC218 Computational Molecular Biology
This lecture was archived from November 30, 1998
Keywords:
Why is Docking Important, Classes of Docking Studies, Lenhoff, Surface Matching, Identifying Cavities, Distribution of Samples
Docking Video
Wednesday, November 24, 1999
Keywords:
Guest Speaker: Scott C. Schmidler
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Protein Folds and Protein Structure Superposition, PDB Size, Tasks, Overview, Classification of Protein Structures, Classes of Protein Structures, A Conceptual Problem, Fold Versus Topology, Database Folds, Automating Structure Classification and Fold Detection, Absolute Orientation Algorithm, Algorithms for Sturcture Superposition, DALI, STRUCTAL, VAST-Vector Alignment Search Tool, Algorithms for Structure Superposition, LOCK-Creating Secondary Structure Vectors, Comparing Secondary Sturcture Vectors, Aligning Secondary Structure Vectors, Step 1: Local Secondary Structure Superposition, Step 3: Core Superposition, LOCK PDB Search: Myoglobin, LOCK PDB Search: Helix-Tum-Helix, 3dSearch, Demonstration, Folds/Architectures
Monday, November 22, 1999
Keywords:
Guest Speaker: Scott C. Schmidler
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Protein Secondary Structure Prediction, Abstracting the problem, 2D prediction, Chou-Fasman prediction, GOR, PHD, helical transmembrane proteins, Predator, SSPAL, Hydrolase, Bayesian Segmentation of Protein Secondary Structure, Probabilistic model, and 3D contacts
Wednesday, November 17, 1999
Keywords:
Guest Speaker: Scott C. Schmidler and Jun S. Liu
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Outline, Sequence Alignment, Statistical models, Multinomial distribution, Motif alignment, Phase-Shift, Fragmentation,
Monitoring Convergece, and PROBE algorithm
Monday, November 15, 1999
Keywords:
Guest Speaker: Thomas D. Wu, M.D., Ph.D.
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Probabilistic Scoring Matrices, Similarity search (BLAST, FASTA), Alignment blocks, Pattern-based sequence analysis
, Two ways of representing patterns
, Basic approaches
, Score-based approach
, Frequency-based approach
, Parameter estimation,
and Pseudocounts
Wednesday, November 10, 1999
Keywords:
Guest Speaker: Russ Altman
Structures, Serine Protease Enzeymes Example, Sequence Motif, 3D Motifs, Radial Graphical Example, Testing for Significance, Radial vs. Oriented Analysis, Calcium Binding Site, Automatic Annotation of new Structures, and Property Arrays
Attn: Please follow the professor as he surfs through the webpages. Thank You.
Monday, November 8, 1999
Keywords:
Markov Models, PROSITE Patterns, eMOTIF Advantages, Evaluating eMOTIFS, Finding eMOTIFS, Identifying Protein Function, ORFs, PSI-BLAST, and eBLOCKS
Attn: Please follow the professor as he surfs through the webpages. Thank You.
Wednesday, November 3, 1999
Keywords:
Multiple Representations of Sequences, Dot Matrix Comparisons, Conserved Residues and Motifs, Probability of x Amino Acid Triplets, PPY, Block Signatures, Transferases, PRINTS, BLOCKS+, Dynamic Prgramming, Threading, Folds, and Sequences
Attn: Please follow the professor as he surfs through the webpages. Thank You.
Wednesday, November 3, 1999
Keywords:
Multiple Representations of Sequences, Dot Matrix Comparisons, Conserved Residues and Motifs, Probability of x Amino Acid Triplets, PPY, Block Signatures, Transferases, PRINTS, BLOCKS+, Dynamic Prgramming, Threading, Folds, and Sequences
Attn: Please follow the professor as he surfs through the webpages. Thank You.
Monday, November 1, 1999
Keywords:
Method for Determining Phylogenies, Properties of Trees, Orthologous Evolution, Gene Duplication, Gene Conversion, Varying Rates of Mutation, Distance Trees, Three Leaf and Four Species Tree, Topologies, UPGMA
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Wednesday, October 27, 1999
Keywords:
Goals of Multiple Sequence Alignment, EMOTIF, Block Signatures for a Protein Family, Hidden Markov Models, Three Protein Alignment, Mapping k-Words to Numbers, Progressive Alignment, Input Sequences, ClustalW, and MACAW
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Monday, October 25, 1999
Keywords:
Sequence Alignment Problem, Needleman-Wunsch Algorithm, The Parametric Approach, Sub-Optimal Alignment Algorithm, Cytochrome C vs Cythochrome C551, Virgon & Argos, Zuker's Method, Immunglobulin Variable Regions
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Wednesday, October 20, 1999
Keywords:
Rapid Similarity Search, BLAST versus Smith & Waterman, cDNA Queries, GAPPED BLAST, PSI-BLAST Alignmnet, Decypher Search Engine, Receiver-Operator Characterisitc
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Monday, October 18, 1999
Keywords:
Redundancy in Genomic and Protein Sequences, Sequence Alignment, Smith-Waterman Homology Search, Computer Time and Space Requirements, Gotoh's Improvement, FastA, BLAST Algorithm, DNA Queries
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Wednesday, October 13, 1999
Keywords:
Sequence Alignment, DNA Dot Matrix, Needleman-Wunsch Algorithm, Dayhoff's Acceptable Point Mutations, Comparison of Scoring Matrices, Smith-Waterman Algorithm, ALION, Gap Program
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Monday, October 11, 1999
Keywords:
Parametric Sequence Analysis, Parameters from Protscale, Protein Chain Flexibility, Helix-Turn-Helix, Weight Matrix, Perceptron Method, Block Signatures, eMATRIX, SEQWeb
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Wednesday, October 6, 1999
Keywords:
A Typical Motif, PROSITE Patterns, Developing Patterns, String Searches, Boyer Moore, Computational Complexity, The Genetic Code, IUPAC Symbols, Regular Expression Syntax, eMOTIF, ORFs & ESTs in Proteomes
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Monday, October 4, 1999
Keywords:
GenBank Database, GenBank Management, DDBJ/EMBL/GenBank Feature Table, GenBank/DDBJ Entry, Structure Database, Sequence Format Conversion Programs, SEQWeb
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Wednesday, September 29, 1999
Keywords:
Internet Applications, Internet Evolution, WWW Traffic, Internet Global Infrastructure, Emerging Problems, Networks and Layers
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Monday, September 27, 1999
Keywords:
BIOC 218: Janet Morrison, MEDLINE, Subject Headings, MeSH Thesaurus, Bootstrap, FULL TEXT Access, and EJournals
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Wednesday, September 22, 1999
Keywords:
Syllabus, Course Availability and Requirements, Bioinformatics, Algorithms, Genomics, Central Paradigm, Smith-Waterman, EMOTIF
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