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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
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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
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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
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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
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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
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3 Apps in iTunes, one in progress
• Molecule World -‐ iPad • Molecule World DNA Binding Lab -‐iPad
• Molecule World for iPhone (no sequences)
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Molecule World DNA-‐binding lab
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Gel electrophoresis lab -‐ in progress
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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
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What is Molecule World?
Molecule World
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Compare elements
What can we do with molecular modeling?
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Demonstrate presence of similar elements - CO2, H2O, Glucose, Fructose, and Sucrose
What can we do with molecular modeling?
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Small chemicals vs. biopolymers (protein, DNA, RNA)
What can we do with molecular modeling?
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Visualize shape: Molecules are not flat
What can we do with molecular modeling?
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Visualize chemical & sequence properties
What can we do with molecular modeling?
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Illustrate molecular interactions
What can we do with molecular modeling?
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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
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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?
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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
© www.digitalworldbiology.com
What is Molecule World?
© www.digitalworldbiology.com
BRCA1 M1775 & CTIP protein – bio-‐ITEST
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BRCA1 – M1775 & CTIP protein phenyalanine
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BRCA1 – M1775 & CTIP protein – bio-‐ITEST
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BRCA1 – M1775 alone – bio-‐ITEST
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BRCA1 – M1775 > R muta7on bio-‐ITEST
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Taste receptors – capsaicin, element coloring
capsaicin
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Taste receptors – capsaicin, charge coloring
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Taste receptors – capsaicin, spider toxin
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Taste receptors – capsaicin
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Taste receptors – capsaicin
© www.digitalworldbiology.com
Taste receptors – wasabi, charge coloring
Allyl isothiocyanate
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