BMB961 - SS17

Concepts in Protein Structure and Modeling
cross-listed as CMSE 890 section 001

InstructorsKaillathe Padmanabhan "Pappan" (
Michael Feig (
Alex Dickson (
Lecture3:00 p.m. - 3:50 p.m. Tuesday in 183 Chemistry
Computer Lab2:00 p.m. - 4:00 p.m. Thursday in 202 Biochemistry
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
GradesBased on proposal presentation (50%) and write-up (50%).

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