BMB961 - FS13

Dynamics and Interactions of Proteins and Nucleic Acids

InstructorsMichael Feig (
Parimal Kar (
Takaharu Mori (
Beibei Wang (
Vivian Fang (
Monika Sharma (
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 8/29 Setup, UNIX, Molecular Graphics Feig
Assigned Reading UNIX overview PDF

Lecture 9/3 Basic data analysis under UNIX Feig
Lab 9/5 Basic UNIX scripting Feig

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
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

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
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

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
J. D. Durrant and J.A. McCammon: Molecular dynamics simulations and drug discovery. BMC Biology (2011) 9(71). PDF
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

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

Lecture 10/8 MMPB/SA free energy estimates Fang
Lab 10/10 Binding free energy estimates Fang
Assigned Reading P. Kollman: Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chemical Reviews (1993) 93, 2395-2417. PDF
P. Kollman: Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models. ACC. Chem. Res. (2000) 33, 889-897. PDF

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
P. Kollman: Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chemical Reviews (1993) 93, 2395-2417 PDF

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
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
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
B. Isralewitz, M. Gao and K. Schulten: Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. (2001) 11, 224 PDF

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

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

Lecture 11/12 Coarse graining II Feig
Lab 11/14 Martini and PRIMO simulations Feig

Lab work 11/19 Class project All
Lab work 11/21 Class project All

Lab work 11/26 Class project All
Thanksgiving 11/28 Holiday

Lab work 12/3 Class project All
Lab work 12/5 Class projectAll

Presentations 12/10 ?
3 pm - 4:30 pm

Presentations 12/12 ?
2:00 pm - 4:00 pm

12/15 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%).

In order to access class contents please connect from a campus computer or use a VPN connection.