Molecular Modeling Course Notes Page 2020

2021 Syllabus


Videos page

Term project description


√∅ Slides Title     When Reading Due
Lecture 1 Intro to proteins  PDF  Tue, Jan 26      
Lecture 2 Where do proteins come from?  PDF  Fri, Jan 29  PDB vid     
Lecture 3 Protein Classification  PDF  Tue, Feb 2      
Lecture 4 Structural Homology  PDF  Fri, Feb 5      
Lecture 5 Barnase/Barstar interactions  PDF  Tue, Feb 9  HW 1    
Lecture 6 Molecular Dynamics  PDF  Fri, Feb 12      
Lecture 7 Normal Mode Analysis  PDF  Tue, Feb 16      
Lecture 8 Electrostatic surfaces  PDF  Fri, Feb 19      
Lecture 9 Force field  PDF  Tue, Feb 23      
Lecture 10 Energy Minimization  PDF  Fri, Feb 26      
Lecture 11 Docking and drug discovery  PDF  Tue, Mar 2      
Lecture 12 Virtual screening, replica exchange MD  PDF  Fri, Mar 5      
Lecture 13 Review  PDF  Tue, Mar 9      
Lecture 14 Midterm  PDF  Fri, Mar 12      
Lecture 15 Nilesh Banavali, strucutre function problems  PDF  Tue, Mar 16      
Lecture 16 Hongmin Li, structure-based drug design  PDF  Fri, Mar 19      
Lecture 17 Covalent drugs and fragment-based drug discovery  PDF  Tue, Mar 23      
Lecture 18 Protein local structure  PDF  Fri, Mar 26      
Lecture 19 Side chain rotamers  PDF  Tue, Mar 30      
Lecture 20 Homology modeling  PDF  Fri, Apr 2  tutorial    
Lecture 21 Voids and waters  PDF  Tue, Apr 6      
Lecture 22 Validation of models  PDF  Fri, Apr 9      
Lecture 23 Phylogenetic analysis  PDF  Tue, Apr 13      
Lecture 24 Quaternary structure  PDF  Fri, Apr 16      
Lecture 25 Modeling nucleic acids  PDF  Tue, Apr 20      
Lecture 26 Protein design workshop  PDF  Fri, Apr 23      
Lecture 27 Student presentations  PDF  Tue, Apr 27      
Lecture 28 Review  PDF  Fri, Apr 30      
    Final exam    TBD      
go to Blackboard

Links etc

 Stereo viewing exercise PDF   HTML   DHFR with TMP              
Sequence 1   Exercise 2.1 (JMOL)   Exercise 1.1   Homework 2  
Exercise 4.2    Homework 1   HW1 protein 1   HW1 protein 2 
 Feb22   SWISS-MODEL   homework 5 
Rotation matrices Realignment exercise deletion exercise  Homework 4 start point: 1a07 
 Lecture 11 exercises   Homework6,7 MOE file   Lecture 12 exercise 
 Anfinsen article  Exercise 3  Exercise4,5 instructions
 1bbzC.pdb  cocaine   Fold-It Rotation
168041592 Protein Design minireview. Exercise 20. SARS2_spike_protein_models B2 TOPS practice HW3 rubric
Termproject:3-fold symmetry generation SARS-CoV-2 pharmacology

Special thanks to Chemical Computing Group for use of the MOE software.

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Thu Apr 23 14:38:27 EDT 2020