What can you learn from molecular modeling?

©
www.digitalworldbiology.com
Molecular
Modeling
Bioinforma7cs,
 
&
Digital
Biology
Sandra
Porter,
PhD

President,
Digital
World
Biology
LLC

Adjunct
Shoreline
Community
College,

Aus7n
Community
College

co-‐PI
Bio-‐Link,
Bio-‐Link.org

©
Bio-‐Link
and
Biotech-‐Careers.org
• Bio-‐Link
is
a
na7onwide
consor7um
of
biotechnology

educa7on
programs
at
colleges
that
oﬀer
2
yr

degrees.

– hJp://bio-‐link.org

• Bio-‐Link
is
commiJed
to
helping
students
gain
the

skills
needed
to
enter
the
biotech/life
science

workforce.

• Course-‐in-‐a-‐Box
-‐
pedagogy,
informa7on
for
teaching

biotech
courses

• Biotech-‐Careers.org
-‐
all
about
biotech
careers

– hJp://biotech-‐careers.org

©
Bioinforma7cs
for
Biotech
Students
Shoreline
Community
College

1
month
(5
weeks)

Hybrid
–
in
person

Students
–

• from
new
to
college
to

bachelors’
degrees,

• some
non-‐na7ve
English

speakers
Aus7n
Community
College

1
semester
(16
weeks)

On-‐line

Students
–

• from
new
to
college
to

bachelors’
degrees,

• some
non-‐na7ve
English

speakers

©
Bioinforma7cs
for
Biotech
Students
1. Molecular
Structures

– Chemical
Bonds

– Physical
proper7es
of
amino
acids,
protein
structure

2. Molecular
Sequences

– BLAST,
alignments,
evolu7on,
sequence
conserva7on

– mRNA
vs
genomic
sequences

3. Gene7c
Varia7on

– stop
codon,
subs7tu7on,
frameshi_

– Eﬀects
of
muta7ons
–
how
might
muta7ons
change
func7on

4.

Variable
–
microarrays,
RNA-‐Seq,
gene
annota7on

©
Challenges
with
Cn3D

• Not
user
friendly

• No
color
keys
or
chemical
names

• All
atoms
same
size

• Can
only
view
ﬁles
from
MMDB,
no
PubChem
or
PDB

• No
op7ons
for
mobile
devices

• Not
easy
to
capture
&
label
images

©
3
Apps
in
iTunes,
one
in
progress
• Molecule
World
-‐
iPad

• Molecule
World
DNA
Binding
Lab
-‐iPad

• Molecule
World
for
iPhone
(no
sequences)

©
Molecule
World
DNA-‐binding
lab

©
Gel
electrophoresis
lab
-‐
in
progress

©
What
is
Molecule
World?
• App
for
molecular
modeling,
Digital
World
Biology
LLC

– slightly
different
versions
for
iPad
&
iPhone,
the
iPad
version
shows

sequences

• User-‐friendly

– color
keys,
image
capture,
control
by
touch

• Can
use
structures
from
different
databases

– NCBI,
PDB,
PubChem

• Uses
updated
informa7on

– atoms
shown
with
different
sizes

– Newer
hydrophobicity
data

• Sequence
viewer
in
iPad
version

©
What
is
Molecule
World?

Molecule
World

©
Compare elements
What can we do with molecular modeling?

©
Demonstrate presence of similar elements - CO2,
H2O, Glucose, Fructose, and Sucrose

©
Small chemicals vs. biopolymers (protein, DNA, RNA)

©
Visualize shape: Molecules are not flat

©
Visualize chemical & sequence properties

©
Illustrate molecular interactions

©
Explore
rela7onship
between
structure
&
func7on
• Learn
about
func7on
by
exploring
structures

– Capsaicin
&
wasabi
receptors

• Visualize
how
a
muta7on
can
aﬀect
func7on

– Breast
cancer
(BRCA1),
drug
resistance

• Protein
interac7ons

– Ebola
Virus
&
an7bodies

©
Addi7onal
resources
–
DWB
Community
Page
Bio-‐ITEST
Gene7c
Tes7ng
Curriculum

– BRCA1
–
case
study,
bioethics,
BLAST
to
learn
who

has
muta7on,
iden7fy
changed
amino
acid

Amgen
Materials
on
PTC
tas7ng
&
evolu7on

– Are
non-‐human
primates
tasters
or
non-‐tasters?

©
Learn
More
• Molecule
World
iPad
and
iPhone
versions,
and

the
Molecule
World
DNA
Binding
Lab
can
be

found
in
the
iTunes
store

• Sign
up
for
our
newsleJer

• Visit
DigitalWorldBiology.com

©
What
is
Molecule
World?

What can you learn from molecular modeling?

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