Lab 8/29 |
Setup, UNIX, Molecular Graphics
Feig |
Assigned Reading |
UNIX overview PDF |
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Lecture 9/3 |
Basic data analysis under UNIX
Feig |
Lab 9/5 |
Basic UNIX scripting
Feig |
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Lecture 9/10 |
Force fields and Monte Carlo simulations
Mori |
Lab 9/12 |
Monte Carlo simulations
Mori |
Assigned Reading |
A. D. Mackerell, Jr.: Empirical Force Fields for Biological Macromolecules: Overview and Issues. J Comput Chem. (2004) 89, 1584-1604 PDF |
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D.-W. Li, S. Mohanty, A. Irback, and S. Huo, Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment, PLoS Computational Biology (2008) 4, e1000238 PDF |
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Lecture 9/17 |
Mode analysis
Feig |
Lab 9/19 |
Normal 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 |
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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 |
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Lecture 9/24 |
Molecular dynamics simulations of biological macromolecules
Sharma |
Lab 9/26 |
Explicit solvent simulations
Sharma |
Assigned Reading |
M. Karplus, J.A. McCammon: Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. (2002) 9(9), 646-652. PDF |
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J. D. Durrant and J.A. McCammon: Molecular dynamics simulations and drug discovery. BMC Biology (2011) 9(71). PDF |
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G. G. Dodson, D. P. Lane and C. S. Verma: Molecular simulations of protein dynamics: new windows on mechanisms in biology. EMBO Rep. (2008) 9(2),144-150. PDF |
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Lecture 10/1 |
Solvent environments and implicit solvent approximations
Kar |
Lab 10/3 |
Implicit solvent simulations
Kar |
Assigned Reading |
B. Roux, T. Simonson: Implicit Solvent Models. Biophysical Chemistry. (1999) 78, 1-20. PDF |
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Lecture 10/8 |
MMPB/SA free energy estimates
Fang |
Lab 10/10 |
Binding free energy estimates
Fang
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Assigned Reading |
P. Kollman: Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chemical Reviews (1993) 93, 2395-2417. PDF |
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P. Kollman: Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models. ACC. Chem. Res. (2000) 33, 889-897. PDF |
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Lecture 10/15 |
Free energy calculations
Feig |
Lab 10/17 |
Free energy calculations
Feig |
Assigned Reading |
D. L. Beveridge and F. M. DiCapua: Free Energy via Molecular Simulation: Applications to Chemical and Biomolecular Systems. Annual Review of Biophyics and Biophysical Chemistry (1989) 18, 431-492 PDF |
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P. Kollman: Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chemical Reviews (1993) 93, 2395-2417 PDF |
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Lecture 10/22 |
Biased sampling techniques
Wang |
Lab 10/24 |
Umbrella sampling and Steered MD simulations
Wang |
Assigned Reading |
G. M. Torrie and J. P. Valleau: Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella Sampling. J. Comput. Phys. (1977) 23, 187 PDF |
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M. Souallie and B. Roux: Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations. Comput. Phys. Comm. (2001) 135, 40 PDF |
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J. Schlitter, M. Engels, P. Kruger, E. U. Jacoby and A. Wollmer: Targeted molecular dynamics simulation of conformational change: application to the T-R transition in insulin. Mol. Simul. (1993) 10, 291 PDF |
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B. Isralewitz, M. Gao and K. Schulten: Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. (2001) 11, 224 PDF |
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Lecture 10/29 |
Replica exchange simulations
Kar |
Lab 10/31 |
Replica exchange simulations
Kar |
Assigned Reading |
A. Mitsutake, Y. Sujita, and Y. Okamoto: Generalized-ensemble algorithms for molecular simulations of biopolymers (Peptide Science) (2001) 60, 96-123 PDF |
MD projects
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Lecture 11/5 |
Coarse graining I
Feig |
Lab 11/7 |
Coarse grained model building
Feig |
Assigned Reading |
S. Riniker, J. R. Allison, and W. F. van Gunsteren: On developing coarse-grained models for biomolecular simulation: a review. Phys. Chem. Chem. Phys. (2012) 14, 12423-12430 PDF |
| Choon-Peng Chng, Lee-Wei Yang: Coarse-Grained Models Functional Dynamics - II. Molecular Dynamics Simulation at the Coarse-Grained Level - Theories and Biological Applications. Bioinformatics and Biology Insights (2008) 2, 171-185 PDF |
| M. G. Saunders and G. A. Voth: Coarse-Graining Methods for Computational Biology. Annu. Rev. Biophys. (2013) 42, 73-93 PDF |
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Lecture 11/12 |
Coarse graining II
Feig |
Lab 11/14 |
Martini and PRIMO simulations
Feig |
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Lab work 11/19 |
Class project
All |
Lab work 11/21 |
Class project
All |
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Lab work 11/26 |
Class project All |
Thanksgiving 11/28 |
Holiday |
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Lab work 12/3 |
Class project All |
Lab work 12/5 |
Class projectAll |
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Presentations 12/10 |
? 3 pm - 4:30 pm |
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Presentations 12/12 |
? 2:00 pm - 4:00 pm |
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12/15 |
Project write-up is due |