Lecture 8/28 |
Proteins and nucleic acids
Feig
|
Lab 8/30 |
Setup, UNIX intro, pyMol tutorial
Feig |
Assigned Reading |
A Conversation with James D. Watson: Scientific American, April 2003,
online |
|
Lecture 9/4 |
Intro to Docking and Scoring
Kuhn |
Lab 9/6 |
Intro to Docking and Scoring
Kuhn |
Assigned Reading |
D. Kitchen, H. Decornez, J. Furr, J. Bajorath: Docking and Scoring in Virtual Screening for Drug Discovery: Methods and Applications, Nature Reviews (2004), 3, 935-949
PDF |
|
I. Kuntz: Structure-Based Strategies for Drug Design and Discovery, Science (1992), 257, 1078-1082
PDF |
|
Lecture 9/11 |
Protein-protein Docking
Zavodszky |
Lab 9/13 |
Protein-protein Docking
Zavodszky |
Assigned Reading |
Zhou HX, Qin S. Interaction-Site Prediction for Protein Complexes: a Critical Assessment.Bioinformatics. 2007 Jun 22; [Epub ahead of print]
PDF |
| Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol. 2002 Feb;12(1):28-35
PDF |
|
Lecture 9/18 |
Flexibility Modeling
Zavodszky |
Lab 9/20 |
Flexibility Modeling
Zavodszky |
Assigned Reading |
Carlson HA. Protein flexibility and drug design: how to hit a moving target.
Curr Opin Chem Biol. 2002 Aug;6(4):447-52
PDF |
| Bonvin AM. Flexible protein-protein docking.
Curr Opin Struct Biol. 2006 Apr;16(2):194-200
PDF |
|
Lecture 9/25 |
Small Molecule Docking
Kuhn |
Lab 9/27 |
Small Molecule Docking
Kuhn |
Assigned Reading |
Slide Quick Guide 3.0a PDF |
|
M. Zavodszky, P. C. Sanschagrin, R. S. Korde, L. A. Kuhn: Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J. Comp. Aid. Mol. Des. (2002) 16, 883-902 PDF |
|
Lecture 10/2 |
Ligand Screening
Kuhn |
Lab 10/4 |
Ligand Screening
Kuhn |
Assigned Reading |
|
|
Lecture 10/9 |
Molecular dynamics simulations
Feig |
Lab 10/11 |
First molecular dynamics simulations
MD projects
are assigned
Feig |
Assigned Reading |
A. D. MacKerell jr.: Empirical Force Fields for Biological Macromolecules: Overview and Issues, J. Comp. Chem. (2004) 25, 1584-1604 PDF |
|
W. F. van Gunsteren, A. E. Mark: Validation of molecular dyanmics simulation, J. Chem. Phys. (1998) 108, 6109-6116 PDF |
|
Lecture 10/16 |
Simulating biological environments
Feig |
Lab 10/18 |
Explicit vs. implicit solvent simulations
Feig |
Assigned Reading |
V. Makarov, B. M. Pettitt, M. Feig: Solvation and Hydration of Proteins and Nucleic Acids: A Theoretical View of Simulation and Experiment, Accounts of Chemical Research (2002) 35, 376-384 PDF |
| B. Roux, T. Simonson: Implicit solvent models, Biophysical Chemistry (1999) 78, 1-20 PDF |
|
Lecture 10/23 |
Trajectory analysis
Feig |
Lab 10/25 |
Trajectory analysis
Feig |
Assigned Reading |
P. Auffinger, L. Bielecki, E. Westhof: The Mg2+ Binding Sites of the 5S rRNA Loop E Motif as Investigated by Molecular Dynamics Simulations, Chemistry & Biology (2003) 10, 551-561 PDF |
| A. Grossfield, S. Feller, M. Pitman: Convergence of molecular dynamics simulations of membrane proteins. Proteins (2007) 67, 31-40 PDF |
|
Lecture 10/30 |
Enhanced sampling
Feig |
Lab 11/1 |
Biased sampling/replica exchange
Feig |
Assigned Reading |
S.Izrailev,S.Stepaniants,B.Isralewitz,D.Kosztin,H.Lu, F.Molnar,W.Wriggers,and K.Schulten: Steered Molecular Dynamics PDF |
| A. Mitsutake, Y. Sugita, and Y. Okamoto: Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers (Peptide Science) (2001) 60, 96-123 PDF |
|
Lecture 11/6 |
Free energy calculations
Feig |
Lab 11/8 |
MMPB/SA analysis
Feig |
Assigned Reading |
P. Kollman: Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chemical Reviews (1993) 93, 2395-2417 PDF |
|
Lecture 11/13 |
Dynamic mode analysis
Feig |
Lab 11/15 |
Mode analysis
Feig |
Assigned Reading |
A. W. van Wynsberghe, Q. Cui: Comparison of Mode Analyses at Different Resolutions Applied to Nucleic Acid Systems. Biophysical Journal (2005) 89, 2939-2949 PDF |
|
AJ Rader. Chakra Chennubhotla, Lee-Wei Yang, and Ivet Bahar: The Gaussian Network Model: Theory and Applications.in "Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems" Eds Qiang Cui and I Bahar, Chapman & Hall / CRC Mathematical and Computational Biology Series, CRC Press, Taylor & Francis Group, 41-64, 2006. PDF |
|
Lecture 11/20 |
MD project discussions
Feig |
Lab 11/22 |
Thanksgiving: NO LAB |
|
Lecture 11/27 |
Student presentations (30 min. each): Linxia Zhang & Ming Wu |
Lecture 11/29 |
Student presentations (30 min. each): Chao Li & Yujie Chen |
|
Lecture 12/4 |
Student presentations (30 min. each): Rahman Saleem & Sean Law |
Lecture 12/6 |
Student presentations (30 min. each): Maryam Sayadi & Cun Liu & Kin Lee |
|
Finals 12/14 |
Project write-up is due |