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About...

An inter-departmental "Structural biology, Computational biology, & Molecular biophysics" special interest group has been formed, consisting initially of a lecture series / j-club by members of the following research groups in the UVa Departments of Chemistry, Chemical Engineering, and Molecular Physiology & Biophysics:

Major Discussion Areas

Spectroscopy

EPR spectroscopy

  • Electron relaxation - Bob Bryant
  • EPR lineshapes and protein dynamics (Cafiso or Columbus lab)
  • Distance measurements (CW and pulse) (Cafiso lab)

NMR spectroscopy

  • NMR-determined protein dynamics; relaxation (Bryant?)
  • NMR structure determination (Columbus)

Diffraction-based methods

  • SAXS and SANS (Columbus lab)
  • X-ray crystallography (Mura lab)
    • Maybe interesting: The "conditional dynamics" approach to ab initio phasing

Computational biology

  • A series of primers on bioinformatics (Mura lab)
    • What are amino acid substitution matrices?
    • How are they used? An intro to sequence alignment
    • Multiple sequence alignment
      • Guide trees
    • Phylogenetic tree estimation
      • Relationship to clustering algorithms
      • Distance-based tree reconstruction
      • Character-based tree sampling
  • Information theory?

Molecular biophysics

Simulation methods

  • An introduction to statistical mechanics & related p-chem background (Mura)
    • Normal mode analysis, entropy, and QHA
    • Classical mechanics...
  • Vanilla MD (all-atom) – Pete R?
  • Force fields (Mura)
  • Advanced topic: Coarse-graining
    • Reduced representations
    • Elastic network models... ENM, GNM, ANM, etc.

Electrostatics calculations

  • An introduction
    • The Poisson-Boltzmann equation (PBE) and approximations (e.g. Debye-Huckel)
    • When to use / not to use (e.g. nonlinear PBE for high charge-density systems)

Biophysical characterization

  • Molecular interactions, binding affinities: isothermal titration calorimetry (ITC), surface plasmon resonance (SPR) [???]
  • Fluorescence: ligand binding assays (FP, FRET, and others...) [Columbus lab?]
  • Analytical Ultracentrifugation [Mura Lab?]

Lecture Series

2012

Winter

  • When: 11 AM January 12
    What: Principles and Theory of Analytical Ultracentrifugation
    Who: Eli Chen (Mura lab)
    Where: Rm 403 PLSB
  • When: 5 PM January 30
    What: Basic Principles of Light Scattering
    Who: Peter Randolph (Mura lab)
    Where: Rm 403 PLSB

2011

Fall

  • When: 6 PM November 2
    What: Fourier Transforms and the Patterson Function
    Who: Peter Randolph (Mura lab)
    Where: Rm C200 PLSB ("new building")
  • When: 5 PM October 3
    What: An Introduction to Fourier Transforms in X-ray Diffraction
    Who: Peter Randolph (Mura lab)
    Where: Rm 304

Summer

Meetings are from 3:30 → 5 PM Fridays in Rm 304 Chemistry this semester, unless otherwise noted. In some cases, if we're not in Rm 304, please look next door in Rm 303 or 305.

In reverse chronological order...

  • When: 3:30 PM August 22
    What: NMR relaxation and dynamics: Some old and some quite new issues
    Who: Bob Bryant (Bryant lab)
    Where: Rm 304
  • When: 3:30 PM July 15
    What: An Introduction to SAXS: What your parents didn't tell you
    Who: Ryan Oliver & the heart breakers (Columbus lab)
    Where: Rm 304
  • When: 3:30 PM July 1
    What: Ligand-binding Equilibria, I
    Who: Tomek Kabzinski (Mura lab)
    Where: Rm 304
  • Never happened...
    • When: TBA
      What: Something Ligand-binding related [TBA]
      Who: Jen Patterson
      Where: TBA
    • When: TBA
      What: What is the sheer joy and utter agony of Biomolecular NMR? Good question.
      Who: Dan Fox, Brett Kroncke and Ryan Lo
      Where: TBA
    • When: TBA
      What: Phylogenetic trees 1, 2, & 3 (or something) [TBA]
      Who: Cam Mura
      Where: TBA

Winter, Spring

Series on hiatus Jan → Jun...

2010

Fall

Series went on hiatus starting Fall semester... (blame Chem4411 & Chem5430)

Summer

Meetings are scheduled for 4 → 5:30 PM in Rm 304 Chemistry this semester, unless otherwise noted. Please note: If no one is in Rm. 190, it means that that room was too crowded and we've relocated to Rm. 304 in the old chemistry build.

In reverse chronological order...

  • When: 4pm, August 20, 2010
    What: MD Simulations: Some Nuts-n-Bolts
    Who: Peter Randolph (Mura lab)
    Where: Chem 304
  • When: 4pm, August 13, 2010
    What: An Introduction to Molecular Dynamics Simulations
    Who: Cam Mura (Mura lab)
    Where: Chem 304
    Update: Presentation slides can be found on the Slides Page.
  • When: 4pm, August 6, 2010
    What: DEER basics: What you always wanted to know, but were too afraid to ask
    Who: Dave Cafiso & the parliament funkadelics (Cafiso lab)
    Where: Chem 304
  • When: 4pm, July 30, 2010
    What: CW EPR of membrane proteins
    Who: Brett Kroncke, Ricardo Flores, & Dan Freed (Columbus lab)
    Where: Chem 304
  • When: 4pm, July 23, 2010
    What: CW EPR basics: soluble vs. membrane proteins
    Who: Linda Columbus & Brett Kroncke (Columbus lab)
    Where: Chem 304
  • When: 4pm, July 16, 2010
    What: T1 relaxation phenomena of spin labels
    Who: Bob Bryant (Bryant lab)
    Where: Chem 190

Calendar


Wikis: Getting started

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