BMB961 - SS17

cross-listed as CMSE 890 section 001

Instructors	Kaillathe Padmanabhan "Pappan" (padmanab@msu.edu) Michael Feig (feig@msu.edu) Alex Dickson (alexrd@msu.edu)
Lecture	3:00 p.m. - 3:50 p.m. Tuesday in 183 Chemistry
Computer Lab	2:00 p.m. - 4:00 p.m. Thursday in 202 Biochemistry
Syllabus	Lecture 1/10 Introduction, Databases (PDB, Uniprot), UNIX Pappan Lab 1/12 Setup, UNIX, Molecular Graphics Pappan Assigned Reading UNIX overview PDF Lecture 1/17 Basic data analysis under UNIX Feig Lab 1/19 Basic UNIX scripting and plotting Feig Lecture 1/24 Sequence alignment and feature analysis Feig Lab 1/26 Sequence analysis Feig Assigned Reading Background on co-evolution analysis FAQ Thesis with detailed background on profile-based sequence aalignments PDF Rost&Sander classic paper on secondary structure predition PDF CASP9 evaluation of disorder prediction PDF Lecture 1/31 Protein structure prediction Feig Lab 2/2 Homology modeling Feig Assigned Reading Comprehensive guide to template-based modeling PDF CASP11 state of the art in structure prediction PDF Lecture 2/7 Modeling of biomolecular structures in the computer Feig Lab 2/9 Structure analysis and electrostatic maps Feig Assigned Reading Perspective on coarse-graining PDF Atomistic force fields PDF Lecture 2/14 Molecular dynamics simulations Grzegorz Nawrocki Lab 2/16 MD of peptides and proteins in water Grzegorz Nawrocki Assigned Reading TBD PDF Lecture 2/21 Enhanced sampling methods Dickson Lab 2/23 Replica exchange or umbrella sampling Dickson Assigned Reading TBD PDF Lecture 2/28 Conformational clustering, networks, and kinetic models Dickson Lab 3/2 Markov state modeling Dickson Assigned Reading TBD PDF 3/6-3/10 spring break Lecture 3/14 Biomolecular interactions and binding free energies Dickson Lab 3/16 Docking and MMPB/SA binding free energy analysis Dickson Assigned Reading TBD PDF Lecture 3/21 Mode analysis Arzu Uyar Lab 3/23 Normal mode analysis Arzu Uyar Assigned Reading TBD PDF Lecture 3/28 Simulations of membrane systems Bercem Dutagaci Lab 3/30 Setup, running, and analysis of membrane-embedded protein simulation Bercem Dutagaci Assigned Reading Membrane protein simulations PDF Enhanced sampling of membrane systems PDF Lecture 4/4 Simulations of nucleic acid systems Maciej Jasinski Lab 4/6 Setup, running, and analysis of nucleic acids Maciej Jasinski Assigned Reading TBD PDF Lecture 4/11 Connecting simulations to experiments Feig Lab 4/13 Simulations vs. experiments Feig Assigned Reading Rotational Diffusion from MD PDF Model free analysis PDF Lab work 4/18 Student presentations All Lab work 4/20 Student presentations All Lab work 4/25 Student presentations All Lab work 4/28 Student presentations All 5/5 Proposal 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
Grades	Based on proposal presentation (50%) and write-up (50%).

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