BMB961 - FS09

Dynamics and Interactions of Proteins and Nucleic Acids

InstructorsMichael Feig (
Shayantani Mukherjee (
Lecture:3:00 p.m. - 3:50 p.m. Tuesday in BCH 502A
Computer Lab:3:00 p.m. - 5:00 p.m. Thursday in BCH 202
Lab 9/3 Setup, UNIX, Molecular Graphics Feig
Assigned Reading UNIX overview PDF

Lecture 9/8 Basic data analysis under UNIX Feig
Lab 9/10 Basic UNIX scripting Feig

Lecture 9/15 Molecular dynamics and Monte Carlo simulations Mukherjee
Lab 9/17 Molecular dynamics simulations of simple liquids Mukherjee
Assigned Reading Feig M: Molecular Simulation Methods: Standard Practices and Modern Challenges (2009) in press PDF
Hu, J. et. al.: Monte Carlo Simulations of Biomolecules: The MC Module in CHARMM. J. Comp. Chem. (2006) 27, 203-216 PDF

Lecture 9/22 Force fields and molecular dynamics simulations of biomolecules Mukherjee
Lab 9/24 First molecular dynamics simulations of biomolecules Mukherjee
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 9/29 Biological solvent environments Feig
Lab 10/1 Explicit 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
M. Feig: Biomolecular Solvation in Theory and Experiment in: Modeling Solvent Environments: Applications to Simulations of Biomolecules, ed. M. Feig, Wiley-VCH (2010) PDF

Lecture 10/6 Implicit solvent models Feig
Lab 10/8 Implicit solvent simulations Feig
Assigned Reading B. Roux, T. Simonson: Implicit solvent models, Biophysical Chemistry (1999) 78, 1-20 PDF

Lecture 10/13 Enhanced sampling Feig
Lab 10/15 Umbrella sampling and Steered Molecular Dynamics Feig
Assigned Reading M. Souaille and B. Roux: Extension to the weighted histogram analysis method: Combining umbrella sampling with free energy calculations. Computer Physics Communications (2001), 135, 40-57 PDF
S.Izrailev,S.Stepaniants,B.Isralewitz,D.Kosztin,H.Lu, F.Molnar,W.Wriggers,and K.Schulten: Steered Molecular Dynamics PDF

Lecture 10/20 Replica exchange simulations Feig
Lab 10/22 Replica exchange simulations Feig
Assigned Reading A. Mitsutake, Y. Sugita, and Y. Okamoto: Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers (Peptide Science) (2001) 60, 96-123 PDF
A. Okur, D. R. Roe, G. L. Cui, V. Hornak, C. Simmerling: Improving convergence of replica-exchange simulations through coupling to a high-temperature structure reservoir. Journal of Chemical Theory and Computation (2007) 3, 557-568 PDF

Lecture 10/27 Free energy calculations Mukherjee
Lab 10/29 MMPB/SA analysis Mukherjee
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
P. Kollman: Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chemical Reviews (1993) 93, 2395-2417 PDF

Lecture 11/3 Coarse graining Feig
Lab 11/5 Coarse grained simulations Feig
Assigned Reading Choon-Peng Chng, Lee-Wei Yang: Coarse-Grained Models Functional Dynamics - II. Molecular Dynamics Simulation at the Coarse-Graned Level - Theories and Biological Applications. Bioinformatics and Biology Insights (2008) 2, 171-185 PDF
MD projects

Lecture 11/10 Dynamic mode analysis Mukherjee
Lab 11/12 Mode analysis Mukherjee
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 "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

Lab work 11/17 Class project Feig/Mukherjee
Lab work 11/19 Class project Feig/Mukherjee

Lab work 11/24 Class project Feig/Mukherjee
Thanksgiving 11/26 Holiday

Presentations 12/1 Rahul Banerjee, Langhua Hu, Qiong Zheng
3 pm - 4:30 pm !

Presentations 12/8 Leann Buhrow, Abu Hassan, Patrick Ochieng, Xiaowei Lu
2:30 pm - 4:30 pm !

Finals 12/18 Project write-up is due
Suggested Texts Andrew R. Leach: Molecular Modelling: Principles and Applications, 2001, Pearson Education
on reserve at BPS library
Tamar Schlick: Molecular Modeling and Simulation: An Interdisciplinary Guide, 2002, Springer
on reserve at BPS library
Kensal van Holde, Curtis Johnson, Shing Ho: Principles of Physical Biochemistry, 2006, Pearson Education
on reserve at BPS library
Other Resources Introduction into protein structure: PDF
Introduction into nucleic acid structure: PDF
GradesBased on project presentation (50%) and write-up (50%).

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