CHEM 451: Topic List

08-25

Course Introduction

Course Syllabus Office Hours Introductory Slides

08-27

Unix, not Eunuchs

Unix Slides Ritchie DM and Thompson K (1974) The UNIX Time-Sharing System Comm ACM 17 365-75

09-01

Shell Games

Shell Games Slides History @ 451

09-03

Shell Games (cont'd)

Bill of Rights Streams Demonstration History @ 451

09-08

Computational Experimentation

Peng RD (2011) Reproducible Research in Computational Science Science 334 1226-7 Sandve GK, Nekrutenko A, Taylor J and Hovig E (2013) Ten Simple Rules for Reproducible Computational Research PLOS Computational Biology 9 e1003285 Baggerly 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 1309-34 Bioinformatics, September, 2026 History @ 451

09-10

Protein Data Bank

Worldwide Protein Data Bank Bernstein 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 80 319-24 Berman HM (2007) The Protein Data Bank: a historical perspective Acta Crystallographica Section A 64 88-95 RCSB PDB PDBselect Hobohm U, Scharf M, Schneider R and Sander C (1992) Selection of representative protein data sets Prot Sci 1 409-17 Dunbrack Lab—PISCES History @ 451

09-15

Protein Folds

Hobohm U, Scharf M, Schneider R and Sander C (1992) Selection of representative protein data sets Prot Sci 1 409-17 PDBselect Dunbrack Lab—PISCES Conte LL, Ailey B, Hubbard TJP, Brenner SE, Murzin AG and Chothia C (2000) SCOP: a Structural Classification of Proteins database Nuc Acid Res 28 257-9 Structural Classification of Proteins Dawson 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 D289-95 Class, Architecture, Topology and Homologous Superfamily History @ 451

09-17

Presentation Graphics

Hobohm U, Scharf M, Schneider R and Sander C (1992) Selection of representative protein data sets Prot Sci 1 409-17 PDBselect Dunbrack Lab—PISCES Conte LL, Ailey B, Hubbard TJP, Brenner SE, Murzin AG and Chothia C (2000) SCOP: a Structural Classification of Proteins database Nuc Acid Res 28 257-9 Structural Classification of Proteins Dawson 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 D289-95 Class, Architecture, Topology and Homologous Superfamily Presentation Graphics Slides Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J Appl Cryst 24 946-50 MolScript MolScript Visual Tutorial Raster 3D History @ 451

09-22

Presentation Graphics (cont'd)

Presentation Graphics Slides Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J Appl Cryst 24 946-50 MolScript MolScript Visual Tutorial Raster 3D History @ 451

09-24

Presentation Graphics (cont'd)

Presentation Graphics Slides Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J Appl Cryst 24 946-50 MolScript MolScript Visual Tutorial Raster 3D History @ 451

09-29

Solvent Accessibility

Picknett T and Davis K (1999) The 100 most-cited articles from JMB J Mol Biol 293 173-6 Lee B and Richards FM (1971) The interpretation of protein structures: estimation of static accessibility J Mol Biol 55 379-400 Wikipedia—Accessible Surface Area naccess History @ 451

10-01

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 1367-1400 Shirley BA, Stannsens P, Hahn U and Pace CN (1992) Contribution of hydrogen bonding to the conformational stability of ribonuclease T1 Biochemistry 31 725-32 Presta LG and Rose GD (1988) Helix Signals in Proteins Science 240 1632-41 Rose GD (2021) Protein folding - seeing is deceiving Protein Science 30 1606–1616 HBPLUS v.3.06 History @ 451

10-06

Midterm Exam

10-08

Secondary Structure

Kabsch W and Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 2577-2637 Frischman D and Argos P (1995) Knowledge-based protein secondary structure assignment Proteins 23 566-79 Scholtz 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 5102-4 Pace CN and Scholtz JM (1998) A helix propensity scale based on experimental studies of peptides and proteins Biophys J 75 422-7 History @ 451

10-13

Sequence Alignment (Global)

Scholtz 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 5102-4 Pace CN and Scholtz JM (1998) A helix propensity scale based on experimental studies of peptides and proteins Biophys J 75 422-7 Slides Needleman SB and Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins JMB 48 443-53 Thompson 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 4673-80 HPr sequences for multiple alignment History @ 451

10-15

No Class—Fall Recess

10-20

Secondary Structure Prediction

Chou PY and Fasman JD (1974) Prediction of protein conformation Biochemistry 13 222-45 Frishman D and Argos P (1997) Seventy-five percent accuracy in protein secondary structure prediction Proteins 27 329-35 PSI-BLAST Tutorial Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices J Mol Biol 292 195-202 History @ 451

10-22

Tertiary Structure Prediction

10-27

Tertiary Structure Prediction (cont'd)

10-29

Molecular Dynamics

11-03

Docking

11-05

Sequence Alignment (Local)

11-10

Sequence Alignment (Local) (cont'd)

11-12

Phylogeny

11-17

High–Throughput Sequencing

11-19

Alignment to a Reference Sequence

11-24

No Class—Thanksgiving Recess

11-26

No Class—Thanksgiving Recess

12-01

Variant Calling

12-03

Various and Sundry Tools

12-08

Using the Literature