451TopicsProblem SetsSeminar
08-26
Course Introduction
Course SyllabusOffice HoursIntroductory Slides
08-28
Unix, not Eunuchs
UNIX SlidesRitchie DM and Thompson K (1974) The UNIX Time-Sharing System Comm ACM 17 365-75
09-02
Shell Games
Shell Games SlidesHistory @ 451
09-04
Shell Games (cont'd)
Bill of RightsStreams DemonstrationHistory @ 451
09-09
Computational Experimentation
Peng RD (2011) Reproducible Research in Computational Science Science 334 1226-7Sandve GK, Nekrutenko A, Taylor J and Hovig E (2013) Ten Simple Rules for Reproducible Computational Research PLOS Computational Biology 9 e1003285Ziemann M, Poulain P and Bora A (2023) The five pillars of computational reproducibility: bioinformatics and beyond Briefings in Bioinformatics 24 1-13Baggerly KA and Coombes KR (2009) Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology The Annals of Applied Statistics 3 1309-34gitChacon S and Straub B (2014) Pro GitHistory @ 451
09-11
Protein Data Bank
Worldwide Protein Data BankBernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T and Tasum M (1977) The Protein Data Bank: A Computer-Based Archival File for Macromolecular Structures Eur J Biochem 80 319-24Berman HM (2007) The Protein Data Bank: a historical perspective Acta Crystallographica Section A 64 88-95RCSB PDBPDBselectHobohm U, Scharf M, Schneider R and Sander C (1992) Selection of representative protein data sets Prot Sci 1 409-17Dunbrack Lab—PISCESHistory @ 451
09-16
Protein Folds
Hobohm U, Scharf M, Schneider R and Sander C (1992) Selection of representative protein data sets Prot Sci 1 409-17PDBselectDunbrack Lab—PISCESConte LL, Ailey B, Hubbard TJP, Brenner SE, Murzin AG and Chothia C (2000) SCOP: a Structural Classification of Proteins database Nuc Acid Res 28 257-9Structural Classification of ProteinsDawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P, Orengo CA and Sillitoe I (2017) CATH: an expanded resource to predict protein function through structure and sequence Nuc Acids Res 45 D289-95Class, Architecture, Topology and Homologous SuperfamilyHistory @ 451
09-18
Protein Folds
Hobohm U, Scharf M, Schneider R and Sander C (1992) Selection of representative protein data sets Prot Sci 1 409-17PDBselectDunbrack Lab—PISCESConte LL, Ailey B, Hubbard TJP, Brenner SE, Murzin AG and Chothia C (2000) SCOP: a Structural Classification of Proteins database Nuc Acid Res 28 257-9Structural Classification of ProteinsDawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P, Orengo CA and Sillitoe I (2017) CATH: an expanded resource to predict protein function through structure and sequence Nuc Acids Res 45 D289-95Class, Architecture, Topology and Homologous SuperfamilyHistory @ 451
09-23
Presentation Graphics
SlidesKraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J Appl Cryst 24 946-50MolScriptMolScript Visual TutorialRaster 3DHistory @ 451
09-25
Presentation Graphics (cont'd)
MolScriptKraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J Appl Cryst 24 946-50MolScript Visual TutorialOceanGate's Titan navigation relied on hand-typed spreadsheetHistory @ 451
09-30
Solvent Accessibility
Picknett T and Davis K (1999) The 100 most-cited articles from JMB J Mol Biol 293 173-6Lee B and Richards FM (1971) The interpretation of protein structures: estimation of static accessibility J Mol Biol 55 379-400Wikipedia—Accessible Surface AreanaccessHistory @ 451
10-02
Hydrogen Bonding
Pauling L (1931) The nature of the chemical bond. Application of results obtained from the quantum mechanics and from a theory of paramagnetic susceptibility to the structure of molecules JACS 53 1367-1400Shirley BA, Stannsens P, Hahn U and Pace CN (1992) Contribution of hydrogen bonding to the conformational stability of ribonuclease T1 Biochemistry 31 725-32Presta LG and Rose GD (1988) Helix Signals in Proteins Science 240 1632-41Rose GD (2021) Protein folding - seeing is deceiving Protein Science 30 1606–16HBPLUS v.3.06History @ 451
10-07
Midterm Exam
Midterm Exam
10-09
Hydrogen Bonding
Pauling L (1931) The nature of the chemical bond. Application of results obtained from the quantum mechanics and from a theory of paramagnetic susceptibility to the structure of molecules JACS 53 1367-1400Shirley BA, Stannsens P, Hahn U and Pace CN (1992) Contribution of hydrogen bonding to the conformational stability of ribonuclease T1 Biochemistry 31 725-32Presta LG and Rose GD (1988) Helix Signals in Proteins Science 240 1632-41Rose GD (2021) Protein folding - seeing is deceiving Protein Science 30 1606–1616HBPLUS v.3.06
10-14
Hydrogen Bonding
Pauling L (1931) The nature of the chemical bond. Application of results obtained from the quantum mechanics and from a theory of paramagnetic susceptibility to the structure of molecules JACS 53 1367-1400Shirley BA, Stannsens P, Hahn U and Pace CN (1992) Contribution of hydrogen bonding to the conformational stability of ribonuclease T1 Biochemistry 31 725-32Hydrogen BondingPresta LG and Rose GD (1988) Helix Signals in Proteins Science 240 1632-41HBPLUS v.3.06History @ 451
10-16
No Class—Fall Recess
10-21
Secondary Structure
Kabsch W and Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 2577-2637Frischman D and Argos P (1995) Knowledge-based protein secondary structure assignment Proteins 23 566-79Scholtz JM, York EJ, Stewart JM and Baldwin RL (1991) A neutral, water-soluble α–helical peptide: the effect of ionic strength on the helix-coil equilibrium JACS 113 5102-4Pace CN and Scholtz JM (1998) A helix propensity scale based on experimental studies of peptides and proteins Biophys J 75 422-7History @ 451
10-23
Sequence Alignment (Global)
SlidesNeedleman SB and Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins JMB 48 443-53Thompson JD, Higgins DG and Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673-80HPr sequences for multiple alignmentHistory @ 451
10-28
Secondary Structure Prediction
Chou PY and Fasman JD (1974) Prediction of protein conformation Biochemistry 13 222-45Frishman D and Argos P (1997) Seventy-five percent accuracy in protein secondary structure prediction Proteins 27 329-35PSI-BLAST TutorialJones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices J Mol Biol 292 195-202History @ 451
10-30
Tertiary Structure Prediction
Protein Structure Prediction CenterScoring FunctionKallberg M, Wang H, Wang S, Peng J, Wang Z, Lu H and Xu J (2012) Template-based protein structure modeling using the RaptorX web server Nature Protocols 7 1511-22Rosetta@HomeTensorFlowTensor Flow Handwritten Number Recognition ExampleJumper J et al. (2021) Highly accurate protein structure prediction with AlphaFold Nature 596 583-91Supplementary Information from Jumper J et al. 2021History @ 451
11-04
Tertiary Structure Prediction
Protein Structure Prediction CenterScoring FunctionKallberg M, Wang H, Wang S, Peng J, Wang Z, Lu H and Xu J (2012) Template-based protein structure modeling using the RaptorX web server Nature Protocols 7 1511-22Rosetta@HomeTensorFlowTensor Flow Handwritten Number Recognition ExampleJumper J et al. (2021) Highly accurate protein structure prediction with AlphaFold Nature 596 583-91Supplementary Information from Jumper J et al. 2021History @ 451
11-06
Docking
Molecular Dynamics SlidesAutoDock4Dihydrofolate Reductase Docking ExampleAutoDock VinaShoichet Laboratory—Docking ScreensHetenyi C and van der Spoel D (2002) Efficient docking of peptides to proteins without prior knowledge of the binding site Prot Sci 11 1729-37Zinc 20Lipinski CA, Lombardo F, Dominy BW and Feeney PJ (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Advanced Drug Delivery Review 23 3-25History @ 451
11-11
Sequence Alignment (Local)
AutoDock4Dihydrofolate Reductase Docking ExampleAutoDock VinaShoichet Laboratory—Docking ScreensHetenyi C and van der Spoel D (2002) Efficient docking of peptides to proteins without prior knowledge of the binding site Prot Sci 11 1729-37Zinc 20Lipinski CA, Lombardo F, Dominy BW and Feeney PJ (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Advanced Drug Delivery Review 23 3-25Pearson WR and Lipman DJ (1988) Improved tools for biological sequence comparison PNAS 85 2444-8Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ (1990) Basic local alignment search tool J Mol Biol 215 403-10The BLAST Sequence Analysis ToolBLAST Command Line Applications User ManualExample 1Example 2Example 3Example 4Example 5PancettaHistory @ 451
11-13
Sequence Alignment (Local) (cont'd)
Pearson WR and Lipman DJ (1988) Improved tools for biological sequence comparison PNAS 85 2444-8Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ (1990) Basic local alignment search tool J Mol Biol 215 403-10The BLAST Sequence Analysis ToolBLAST Command Line Applications User ManualExample 1Example 2Example 3Example 4Example 5PancettaPrimer3Basic Primer3 Input FilePertsemlidis A and Fondon JW (2001) Having a BLAST with bioinformatics (and avoiding BLASTphemy) Genome Biology 2 1-10FASTA ScramblerHistory @ 451
11-18
Phylogeny
Example 1Example 2Example 3Example 4Example 5PancettaFASTA ScramblerPertsemlidis A and Fondon JW (2001) Having a BLAST with bioinformatics (and avoiding BLASTphemy) Genome Biology 2 1-10Primer3Basic Primer3 Input FileFelsenstein J (1988) PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITY Ann Rev Gen 22 521-65PHYLIP PHYLIP—DocumentationCytochrome C ExampleMyoglobin ExampleThe Newick tree formatHistory @ 451
11-20
Phylogeny
Felsenstein J (1988) PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITY Ann Rev Gen 22 521-65PHYLIP PHYLIP—DocumentationCytochrome C ExampleMyoglobin ExampleThe Newick tree formatHistory @ 451
11-25
No Class—Thanksgiving Recess
11-27
No Class—Thanksgiving Recess
12-02
High–Throughput Sequencing
DNA Sequencing SlidesAmbardar S, Gupta R, Trakroo D and Vakhlu J (2016) High Throughput Sequencing: An Overview of Sequencing Chemistry Indian J Microbiol 56 394-404Illumina Chemistry DemonstrationLi H and Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform Bioinformatics 25 1754-60Saccharomyces cerevisiae Reference GenomeEMBI SRA DescriptionSaccharomyces cerevisiae Sequencing Run ResultsNCBI Sequence Read ArchiveHistory @ 451
12-04
Alignment to a Reference Sequence
DNA Sequencing SlidesAmbardar S, Gupta R, Trakroo D and Vakhlu J (2016) High Throughput Sequencing: An Overview of Sequencing Chemistry Indian J Microbiol 56 394-404Illumina Chemistry DemonstrationLi H and Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform Bioinformatics 25 1754-60Saccharomyces cerevisiae Reference GenomeEMBI SRA DescriptionSaccharomyces cerevisiae Sequencing Run ResultsNCBI Sequence Read ArchiveHistory @ 451
12-09
Variant/SNP Calling
DNA Sequencing SlidesAmbardar S, Gupta R, Trakroo D and Vakhlu J (2016) High Throughput Sequencing: An Overview of Sequencing Chemistry Indian J Microbiol 56 394-404Illumina Chemistry DemonstrationLi H and Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform Bioinformatics 25 1754-60Saccharomyces cerevisiae Reference GenomeEMBI SRA DescriptionSaccharomyces cerevisiae Sequencing Run ResultsNCBI Sequence Read ArchiveThe 1000 Genomes Project Consortium (2015) A global reference for human genetic variation Nature 526 68-74Slatkin M and Racimo F (2016) Ancient DNA and human history PNAS 113 6380-7Heroin Addicted Rat Sequencing Runs Report (NIH)Heroin Addicted Rat Sequencing Runs Report (EBI)Rattus norvegicus Indexed Genome (Rattus_norvegicus.mRatBN7.2 dna_smtoplevel)Student Course EvaluationsHistory @ 451
12-16
Final Exam—18:00
Final Exam
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