BMB961 - FS11

Dynamics and Interactions of Proteins and Nucleic Acids

InstructorMichael Feig (
Lecture:3:00 p.m. - 3:50 p.m. Tuesday in BCH 502A
Computer Lab:2:00 p.m. - 4:00 p.m. Thursday in BCH 202
Lab 10/20 Setup, UNIX, Molecular Graphics
Assigned Reading UNIX overview HTML

Lecture 10/25 Molecular dynamics simulations
Lab 10/27 Molecular dynamics simulations of water
Assigned Reading Feig M: Molecular Simulation Methods: Standard Practices and Modern Challenges in Computational Modeling in Lignocellulosic Biofuel Production, eds. Mark R. Nimlos, Michael Crowley, ACS (2010) PDF

Lecture 11/1 Biomolecular simulations
Lab 11/3 Molecular dynamics simulations of biomolecules
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 11/8 Biological solvent environments
Lab 11/10 Implicit solvent treatments
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
B. Roux, T. Simonson: Implicit solvent models, Biophysical Chemistry (1999) 78, 1-20 PDF

Lecture 11/15 Free energy calculations
Lab 11/17 Free energy calculations
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 11/22 Coarse graining
Assigned Reading 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

Lecture 11/29 Dynamic mode analysis
Lab 12/1 Mode analysis
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 12/8 Project presentations

Finals 12/16 Project write-up is due

Suggested Texts Andrew R. Leach: Molecular Modelling: Principles and Applications, 2001, Pearson Education
Tamar Schlick: Molecular Modeling and Simulation: An Interdisciplinary Guide, 2002, Springer
Kensal van Holde, Curtis Johnson, Shing Ho: Principles of Physical Biochemistry, 2006, Pearson Education
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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