| 1/9/17 |
Introduction |
slides
|
|
|
|
Ron Dror |
|
| 1/11/17 |
Simulation of drug targets and simulation analysis |
slides
|
1. Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs
2. Identifying localized changes in large systems: Change-point detection for biomolecular simulations
|
|
|
Ron Dror |
|
| 1/16/17 |
Guest talk:
Virtual reality
for structural
biology (Optional) |
|
|
|
|
Eli Groban (Autodesk) |
|
| 1/18/17 |
Using multiplayer online video games for structure prediction and design |
intro
slides
|
1. Predicting protein structures with a multiplayer online game
2. RNA design rules from a massive open laboratory
3.
Principles
for
predicting
RNA
Secondary
Structure
Design
Difficulty
|
a. Scientific rigor through videogames
b. Crystal
structure
of a
monomeric
retroviral
protease
solved by
protein
folding
game
players
c. Algorithm
discovery
by protein
folding
game players
|
|
Seth
Hildick-Smith
Jesse
Min
Meera Srinivasan
|
1. Lawrence
Murata
1. Julia Wang
2. Philip Scott
DiGiacomo
2. Pavitra Rengarajan
3. Anika Naidu
|
| 1/23/17 |
Coevolution
methods for
predicting
structure from
large numbers of
genetic
sequences |
intro
slides
|
1. Three-Dimensional
Structures
of
Membrane
Proteins
from
Genomic Sequencing
2. Improved
Contact
Predictions
Using the
Recognition
of Protein Like Contact Patterns
3.
Accurate
De Novo
Prediction
of Protein
Contact
Map by
Ultra-Deep
Learning Model
|
a. Large
scale
determination
of
previously
unsolved
protein
structures
using
evolutionary
information
b. From
residue
coevolution
to protein
conformational ensembles and functional dynamics
c. Protein
structure
prediction
from
sequence
variation
|
|
Jason Wang
Kaitlyn
Lagattuta
Phillip DiGiacomo
|
1. Anika
Naidu
1. Ambika Acharya
2. Seth
Smith
3. Mila
Shultz
3. Adithya Ganesh
|
| 1/25/17 |
Modern protein
design |
intro
slides
|
1. De
novo
design of
a
transmembrane
Zn2+-transporting
four-helix
bundle
2. Accurate
design of
megadalton-scale
two-component
icosahedral
protein
complexes
3. Accurate
de novo
design of
hyperstable
constrained peptides
|
a. Computational
design of
ligand-binding
proteins
with high
affinity
and selectivity
b. Principles
for
designing
ideal
protein
structures
|
|
Anika Naidu
Kevin
Goncalves
Mila Shultz
|
1. Karen Lee
1. Julia
Wang
2. Heejo
Choi
2. Ambika
Acharya
3. Will Hang
|
| 1/30/17 |
Machine
learning for
structured-based
virtual screening |
intro
slides
|
1. AtomNet:
A Deep
Convolutional
Neural
Network
for
Bioactivity
Prediction
in
Structure-based
Drug
Discovery
2.
Learning
Deep
Architectures
for
Interaction
Prediction
in
Structure-based
Virtual
Screening
3.
Machine-learning
scoring
functions
to improve
structure-based
binding
affinity
prediction
and
virtual
screening
|
a. Convolutional Networks on Graphs for Learning Molecular Fingerprints
b.
A machine
learning
approach
to
predicting
protein-ligand
binding
affinity
with
applications
to
molecular
docking.
c. Boosting
Docking-based
Virtual
Screening
with Deep
Learning
|
|
Victor
Storchan
Christopher
Vo
Lawrence
Murata
|
1. Jason
Wang
1. Daniel
Fernandes
2. Mila
Shultz
2. Alex Sly
3. Kaitlyn
Lagattuta
3. Anika Nagpal
|
| 2/1/17 |
Improving
virtual screening
through
physics-based methods |
intro
slides
|
1.
Incorporation
of protein
flexibility
and
conformational
energy
penalties
in docking
screens to
improve
ligand discovery
2. Alchemical
free
energy
methods
for drug
discovery:
progress
and
challenges
3. Accurate
and
Reliable
Prediction
of
Relative
Ligand
Binding
Potency in
Prospective
Drug
Discovery
by Way of
a Modern
Free-Energy
Calculation
Protocol
and Force
Field
|
a. Alchemical
Free
Energy
Calculations:
Ready for
Prime
Time?
|
|
Wisam Reid
Miguel
Camacho-Horvitz
Karen Lee
|
1. Axel Sly
1. Seth Hildick-Smith
2. Hugo
Kitano
2. Pavitra Rengarajan
3. Kaitlyn Anne
Lagattuta
3. Will Hang
|
| 2/6/17 |
New methods
for solving tough
crystal structures |
intro
slides
|
1. Super-resolution biomolecular crystallography with low-resolution data
2.
Guiding
Belief
Propagation
using
Domain
Knowledge
for
Protein-Structure
Determination
|
a.
Assessing
and
maximizing
data
quality in
macromolecular crystallography
b. A grid-enabled web service for low-resolution
crystal
structure refinement
c. Deformable
elastic
network
refinement
for
low-resolution
macromolecular
crystallography
d. Enabling X-ray
free
electron
laser
crystallography
for
challenging
biological
systems from a limited number of crystals
e. Improving
the
Accuracy
of
Macromolecular
Structure
Refinement
at 7Å
Resolution
f. Linking
Crystallographic
Model and
Data
Quality
g.
Accurate
macromolecular
structures
using
minimal
measurements
from X-ray
free-electron
lasers
|
|
Daniel
Byrnes
Hari
Ravichandran
|
1. Masood
Malekghassemi
1. Meera
Srinivasan
1. Daniel
Hogan
2. Jesse Min
2. Jenifer Brown
|
| 2/8/17 |
Markov state models for molecular dynamics simulations |
intro
slides
|
1. Everything
you wanted
to know
about
Markov
State
Models but
were
afraid to
ask
2. Markov
state
models of
biomolecular
conformational
dynamics
3.
HTMD:
High-Throughput
Molecular
Dynamics
for
Molecular
Discovery
|
a.
Improvements
in Markov
State
Model
Construction
Reveal
Many
Non-Native
Interactions
in the
Folding of
NTL9
b.
Markov
State
Models
Provide
Insights
into
Dynamic
Modulation
of Protein
Function
|
|
Michael
Maduabum
Adithya
Ganesh
Axel Sly
|
1. Daniel
Byrnes
1. Miguel
Camacho-Horvitz
2. Hugo
Kitano
2. Phillip
DiGiacomo
3. Victor
Storchan
3. Christopher Vo
|
| 2/13/17 |
RNA Structure Prediction & Design of Protein/Nucleic Acid Complexes |
intro
slides
|
1. Computational
design of
co-assembling
protein–DNA
nanowires
2. Accurate
SHAPE-directed
RNA secondary
structure
modeling,
including
pseudoknots
|
a.
3D RNA and
Functional
Interactions
from
Evolutionary Couplings
|
|
Julia Wang
Ambika
Acharya
|
1. Alex
Yoshikawa
1. Heejo
Choi
1. Jason
Wang
2. Meera
Srinivasan
2. Michael Maduabum
|
| 2/15/17 |
Computational methods for single-particle electron microscopy |
intro
slides
|
1. A
Bayesian
View on
Cryo-EM
Structure
Determination
2.Trajectories
of the
ribosome
as a
Brownian
machine
|
a. Advances
in
Single-Particle
Electron
Cryomicroscopy
Structure
Determination
applied to
Sub-tomogram
Averaging
b. A
Primer to
Single-Particle
Cryo-Electron
Microscopy
c. Dynamics
in cryo EM
reconstructions
visualized with
maximum-likelihood
derived variance
maps
d. Prevention
of
overfitting
in cryo-EM
structure
determination
e.Molecular
dynamics-based
refinement
and
validation
for sub-5
A?
cryo-electron
microscopy
maps
f.Flexible
Fitting of
Atomic
Structures
into
Electron
Microscopy
Maps Using
Molecular
Dynamics
Simulation
|
|
Hugo Kitano
Daniel Hogan
|
1. Hari
Ravichandran
1. Jesse Min
1. Jasmine
Johnson
2. Daniel
Byrnes
2. Leo
Keselman
2. Wisam
Reid
|
| 2/20/17 |
No Class |
|
|
|
|
|
|
| 2/22/17 |
Protein-protein interactions |
intro
slides
|
1. Structure-based
prediction
of
protein–protein
interactions
on a
genome-wide
scale
2.
Panorama
of ancient
metazoan
macromolecular complexes
|
a.Networks
of bZIP
Protein-Protein
Interactions
Diversified
Over a
Billion
Years of
Evolution
b. Interactome3d:
adding
structural
details to
protein
networks
|
|
Anika Nagpal
Masood
Malekghassemi
|
1. Christine
Yiwen Yeh
1. Jenifer
Brown
1. Raj Raina
2. Hari
Ravichandran
2. Kevin Goncalves
|
| 2/27/17 |
Integrative modeling
of molecular
complexes |
intro
slides
|
1.
Determining the
architectures of
macromolecular
assemblies
2. Conformational
States of
Macromolecular
Assemblies Explored by
Integrative Structure
Calculation
3.
Molecular architecture
of the yeast Mediator complex
|
a. A strategy for
dissecting the
architectures of
native macromolecular
assemblies
b. Outcome of the First wwPDB Hybrid/Integrative Methods Task
Force Workshop
|
|
Christine Yiwen
Yeh
Delaney Sullivan
Jenifer Brown
|
1. Alex Yoshikawa
1. Kevin Goncalves
2. Jenifer Brown
2. Masood
Malekghassemi
3. Daniel
Fernandes
3. Raj Raina
|
| 3/1/17 |
Three-dimensional genome architecture |
intro
slides
|
1. Genome
architectures
revealed
by
tethered
chromosome
conformation
capture
and
population-based
modeling
2. A
3D Map of
the Human
Genome at
Kilobase
Resolution
Reveals
Principles
of
Chromatin
Looping
|
a. Three-dimensional
genome
architecture:
players and
mechanisms
b. Chromatin
extrusion
explains
key
features
of loop
and domain
formation
in
wild-type
and
engineered
genomes
c. Comprehensive
mapping of
long-range
interactions
reveals folding
principles of the
human
genome
|
|
Brad Krajina
Alex Yoshikawa
|
1. Anika
Nagpal
1. Delaney
Sullivan
2. Delaney
Sullivan
2. Christine
Yiwen Yeh
|
| 3/6/17 |
Machine learning on microscopy images |
intro
slides
|
1. Automated
Learning
of
Subcellular
Variation
among
Punctate
Protein
Patterns
and a
Generative
Model of
Their
Relation
to
Microtubules
2. Scoring
diverse
cellular
morphologies
in
image-based
screens
with
iterative
feedback
and
machine
learning
3.
Fast,
accurate
reconstruction
of cell
lineages
from
large-scale
fluorescence
microscopy data
|
|
|
Ramin Ahmari
Will Hang
Pavitra
Rengarajan
|
1. Leo
Keselman
1. Christopher
Vo
2. Brad
Krajina
2. Miguel
Camacho-Horvitz
3. Victor
Storchan
|
| 3/8/17 |
Cellular-level simulation |
intro
slides
|
1. ReaDDy
- A
Software
for
Particle-Based
Reaction-
Diffusion
Dynamics
in Crowded
Cellular
Environments
2.
Decoding
Information
in Cell
Shape
3. Computational
modeling
of
cellular
signaling
processes
embedded
into
dynamic
spatial
contexts
|
a. Fast monte carlo simulation methods for biological reaction-diffusion systems in solution and on
surfaces
b. ReaDDyMM:
Fast
Interacting
Particle
Reaction-Diffusion
Simulations
Using
Graphical
Processing
Units
|
|
Heejo Choi
Jasmine
Johnson
Raj Raina
|
1. Michael
Maduabum
1. Daniel
Fernandes
2. Karen Lee
2. Ramin
Ahmari
3. Wisam Reid
|
| 3/13/17 |
Superresolution fluorescence microscopy |
intro
slides
|
1. Faster
STORM
using
compressed
sensing
2.
Lattice
light-sheet
microscopy:
Imaging
molecules
to embryos
at high
spatiotemporal
resolution
|
a.
Super-Resolution
Fluorescence
Imaging with
Single
Molecules
b.
Robust
single-particle
tracking in
live-cell
time-lapse
sequences
|
|
Leonid
Keselman
Daniel Fernandes
|
1. Lawrence Lin
Murata
1. Daniel
Hogan
2. Ramin
Ahmari
2. Brad
Krajina
2. Jasmine Johnson
|
| 3/15/17 |
TBD |
|
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