Advanced Biofuels Markets

November 2010

Alan Shaw, Ph.D.

President & CEO
Forward-Looking Statements
These slides and the accompanying oral presentation contain forward-looking statements that
involve risks and uncertainties. These statements relate to future events or our future financial
or operational performance and involve known and unknown risks, uncertainties and other
factors that could cause our actual results, levels of activity, performance or achievement to
diff materially
differ t i ll from
f those
th expressedd or implied
i li d by
b these
th forward-looking
f d l ki statements.
t t t Forward-
F d
looking statements include all statements that are not historical facts. In some cases, you can
identify forward-looking statements by terms such as “may,” “will,” “should,” “could,” “would”,
“expects,” “plans,” “anticipates,” “believes,” “estimates,” “projects,” “predicts,” “potential,” or
the negative
g of these terms, and similar expressions
p and comparable
p terminology
gy intended to
identify forward-looking statements. These forward-looking statements represent our estimates
and assumptions only as of the date hereof, and, except as required by law, we undertake no
obligation to update or revise publicly any forward-looking statements, whether as a result of
new information, future events or otherwise.

Other factors that could materially affect actual results, levels of activity, performance or
achievements can be found in Codexis’ Quarterly Report on Form 10-Q dated November 4, 2010,
including under the caption “Risk Factors.” If any of these risks or uncertainties materialize, or
if our underlying assumptions prove to be incorrect, actual results, levels of activity,
performance or achievement may vary significantly from what we projected.

Our logo, “Codexis,” and other trademarks or service marks of Codexis, Inc. appearing in this
presentation are the property of Codexis, Inc. This presentation contains additional trade
names, trademarks and service marks of other companies. We do not intend our use or display
of other companies’ trade names, trademarks or service marks to imply relationships with, or
endorsement or sponsorship of us by, these other companies.
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Biobased Solutions for the Low Carbon Economy

Making industrial processes faster, cleaner and more efficient

Company Background Proprietary Technology Diverse, Growing Revenue

 Founded in 2002
 Spun out of Maxygen
 290 employees
 Global operations – U.S.,
Hungary and Singapore
 A leader in directed  Product sales to leading
evolution pharma companies
 Significant cost and  Provider of intermediates
speed to market benefits for Lipitor
vs. chemistry
 One platform…multiple
markets  Strategic
g collaboration
with Shell for biofuels

2
Validated by Global Industry Leaders

Industry-leading
Customers and
Partners

Industry-leading
Investors

(Revenue, $ in millions)

$100+
$83
$50
Rapid Growth $25
$12

(1)
FY06 FY07 FY08 FY09 FY10E

3
(1) FY10 Guidance as of October 28, 2010
Company Highlights

Disruptive and proven technology platform

Opportunities in multiple major and growing markets

Pharmaceutical business demonstrates commercial scalability

Strategic collaboration with Shell in biofuels

Business model drives attractive financial profile

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Disruptive and Proven
Technology Platform

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Components of Our Disruptive Technology Platform

Bioinformatics
C1 Expression
Enzyme Gene
Production Shuffling--Systems
Shuffling
System Evolution

Cutting edge Biology

Cutting-edge

Scale
Up Cellular Engineering

Process Engineering
Systems & Synthetic
Biology

C bi i
Combining the
th Best
B t off Silicon
Sili V
Valley
ll and
d Bi
Biotechnology
t h l

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DNA Shuffling - Evolution Tools

Protein Pathway Genome

Evolution Evolution Evolution
Enzymes
Wild Wild
Type Low Yield, Type
Enzyme High Cost Genome
Product

DNA “Omics” Genome

Shuffling Analysis
y Shuffling
g
Process & Shuffling Process
Process

Improved IImproved
d Improved
Enzyme Enzymes
Genome

High Yield,
Low Cost
Product

7
Our Technology Platform in Action
Significantly improved performance
Wild-type enzyme with limited activity
using our technology platform
Relative Activity

Relative Activity
Codexis
Technology

• Lowers capital costs • Lowers operating costs

• Reduces downtime • Speeds time-to-market
• Flexible feedstock • Dramatically improves performance

F t Cheaper,
Faster, Ch Cleaner
Cl

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Advanced Biofuels

Codexis Shell Partnership

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Codexis and Shell… A Powerful Solution
Next-generation
Feedstock / Mills Path to Market
Conversion Technology

Refining
Sugar
g Cane and Bagasse
g

Distribution
Wheat Straw

Other Biomass Sales

High Capital Intensity Capital Efficient Biology High Capital Intensity

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Path to Biofuel Commercialization

Proprietary directed
e ol tion technolog
evolution technology Sugar cane ethanol

Biofuel
commercialization
with Shell
Proven pharma platform
success and scale up Cellulosic ethanol

Partnered with leading

global transportation Drop-in diesel
fuels vendor

Done Next Steps

p Future

11
Royal Dutch Shell Strategy Update – March 16, 2010

Source: Royal Dutch Shell, March 2010.

12
Shell Cosan $12B JV

 Shell is the world’s largest biofuels distributor

 JV would be Brazil’s
Brazil s largest ethanol producer
 2B liters ethanol production capacity/year

 23 sugar mills, 60M tons crushing capacity/year

 4500 retail stations

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JV: Future Potential Use of Codexis Technology

 Codexis technology platform jump-start to next

generation biofuels program
 Can accelerate Codexis commercialization

 1st g
gen sugarcane
g ethanol: new optimized
p biocatalysts
y
 2nd gen cellulosic ethanol: custom biocatalysts using
sugarcane residue now burned or put in landfill
 3rd gen biodiesel/biohydrocarbon fuels: custom
biocatalysts

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Media: Future of Biofuels

 The Shell Cosan

joint venture will be
the “world’s largest
Oct. 30, 2010 biofuels operation”
Biofuels are back.  Capacity of “more
more
This time they than 2B liters a year”
might even work.
 Codexis biofuels-
enabling partner

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Drop-in Diesel

 Uses Codexis disruptive

technology platform
 No other company can
combine state-of-the-art
state of the art Gene
Shuffling--Systems
Shuffling
cellular engineering/systems Evolution
& synthetic biology with
Codexis proprietary shuffling
technology
Scale
Cellular Engineering
 Early stage project achieving Up

results on par with published

competitive efforts.
Systems & Synthetic
Biology

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The New Light, “Sweet” Crude

2 Global Markets

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Additional Major Market Opportunities

Multiple Markets…One
Markets One Platform

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 NASDAQ: CDXS

CONFIDENTIAL 19