Good day, ladies and gentlemen, and welcome to Codexis Third Quarter of 2012 Earnings Conference Call. This call is being webcast live on the Investors section of Codexis’ website at codexis.com. This call is property of Codexis and any recording, reproduction or transmission of this call without expressed written consent of Codexis is strictly prohibited. As a reminder, today’s call is being recorded. You may also listen to a webcast replay of this call by going to the Investors section of Codexis’ website. I would now like to turn the call over to Mr. Doug Sheehy, Codexis’ General Counsel. Please proceed.

Thank you and good afternoon. Today after market close, we announced our fiscal third quarter 2012 financial results. The press release is available on the Investors page of our website at codexis.com. With me today is John Nicols, our President and Chief Executive Officer, and David O’Toole, our Senior Vice President and Chief Financial Officer. During the course of today’s call, management will make a number of forward-looking statements. These forward-looking statements include our forecast for 2012 revenue, adjusted EBITDA, year-end cash and total pharmaceutical product sales; our ability to obtain rights to CodeXyme in Brazil, our expectation for development funding from Raízen; startup timelines for the CodeXol demo plant; the development of a market for cellulase enzymes; expected improvements in our operational productivity and efficiency; the effect of the new Arch agreement on our financial results; improvements in our pharmaceutical product pipeline from our Merck relationship; and profitable sales growth in our pharmaceutical business. These forward-looking statements are based on assumptions and are subject to risks and uncertainties that could cause actual results to differ significantly from those projected. Given these risks and uncertainties, you should not place undue reliance on these forward-looking statements. Please refer to our Form 10-Q filed with the Securities and Exchange Commission today, November 7, 2012 for some of the important risk factors that could cause actual results to differ materially from the forward-looking statements made on this call. Except as required by law, we disclaim any obligation to publicly update or revise any forward-looking statements to reflect events or circumstances that occur after this call. During today’s call, we will discuss certain non-GAAP financial measures for comparison purposes only. The non-GAAP amount of adjusted EBITDA is calculated by adding depreciation, amortization, net interest expense, income taxes, impairment of marketable securities and stock compensation to our net loss. This non-GAAP measure is an addition to, not a substitute for or superior to, measures of financial performance prepared in accordance with GAAP. Please refer to our press release today for a reconciliation of the non-GAAP financial measures to GAAP. Now, I’d like to turn the call over to John Nicols.

Good afternoon and thank you for joining us. The third quarter was an important phase in Codexis’ transition as we work to best position the company for long-term growth and value creation. We remain focused on our key priorities of growing the profitability of our leading pharmaceutical products and services business, and driving our unique technology platform towards commercialization in the fuels and chemicals markets. During my first full quarter as CEO of Codexis, we made significant progress in moving the company towards these goals. Before getting into financial and business specifics for the quarter, let me highlight the hard but crucial work this quarter of strategically realigning the company for our forward growth strategy following the loss of Shell funding. As promised, we did not waste any time enacting to reduce costs to ensure that these reductions timed as closely as possible to the completion of our Shell collaboration and loss of R&D funding. Mission accomplished. These actions included the difficult decisions to reduce head count by approximately 130 employees in Redwood City and the closure of our Singapore facility resulting in a reduction of approximately 45 employees. This right sizing of our organization is expected to enable marked improvements in the productivity and efficiency of our operations and is designed to maintain the most optimal mix of R&D resources for our development programs in pharma, fuels, chemicals. Additionally, a key priority has been to solidify our senior management team with the right mix of capabilities to lead Codexis into a new phase of commercial execution. Again mission accomplished. As you know, I joined Codexis in June after a 22-year career of various leadership roles at Albemarle; shortly thereafter in September we named our new CFO, David O’Toole, who joins us on today’s call. David brings with him over…

Thanks, David. At this point I’ll provide some highlights of our successes in our key business segments. I will begin with our CodeXyme Cellulase Enzymes for the hydrolysis of cellulosic biomass to sugars. Let me start with how proud I am about the great results from our R&D team developing CodeXyme. During the last several months, we have gained evidence from an independent assessment that validates that our cellulase enzymes are equal to or better than the leading enzyme products available today. In just three years time, we have been able to catch up to much better capitalized, longer standing cellulase producers. This progress gives us a seat at the table for what I believe will be the largest development for the global enzyme industry over the remainder of this decade, that being the new enzyme application to convert second generation biomass feedstocks into fermentable cellulosic sugars or fuels and chemicals. Truly this is a great milestone for Codexis, especially now that we have gained the rights from Shell to market CodeXyme to third parties. In previous quarters, our ability to address the fuels market, the largest application of CodeXyme, was limited to our partners Shell and Raízen. On August 31, we achieved the key milestone in building the long-term value of CodeXyme by securing from Shell an agreement that grants us broad rights to commercialize CodeXyme for biofuels applications worldwide. Codexis’ marketing rights exclude Brazil as Raízen currently has exclusive rights to the CodeXyme technology in that country. We continue to engage in discussions with Raízen, the world’s largest producer of ethanol from sugarcane and our largest shareholder, about our best path forward for monetizing our CodeXyme technology in Brazil. Those discussions center around Codexis obtaining rights to market CodeXyme broadly within the Brazilian fuels market like we have…

Certainly. (Operator Instructions) And our first question is from the line of Patrick Jobin from Credit Suisse. Patrick Jobin – Credit Suisse: Hi, good afternoon, guys.

Hey, Patrick. David O’Toole: Good afternoon. Patrick Jobin – Credit Suisse: Just wanted to touch on 2013, any idea as far as your growth outlook there and kind of how you’re going to position the company for 2013?

Yeah, let me start and David please fill in as you feel appropriate. 2013, obviously, will be a year without any funding for the CodeXyme from Shell unlike 2012. So, the revenue outlook from that segment will be down accordingly. Our pharmaceutical business has had an off year in 2012 versus the recent past. We expect that the revenue outlook for that business taking into account the new relationship with Arch will be up especially on the profit side for 2013. And then on the cost side, you’ve noted the test work that we’ve done to dramatically reduce the cost of our operations as we end this year and go into next year. Generally, we are set up to give you much clear guidance as we have in the past in the beginning of 2013 after we close out our fourth quarter earnings. Patrick Jobin – Credit Suisse: Okay. And then on the CodeXyme outlook, now that you are somewhat more liberated to engage other parties, can you may be give us the sense as to number of discussions that are ongoing and when from a timing perspective we might expect those to convert to either announcements or potential revenue?

Yeah. Patrick Jobin – Credit Suisse: And then may be just highlight the competitive position that you see CodeXyme right now?

Okay. So there’s three questions in there. First question, we are engaged in ballpark, a handful maybe slightly more different conversations with commercialization partners. So we’re having good conversations. The market is generally very receptive to the technology position that we’ve developed under the Shell arrangement. I highlighted in the call that we’ve gotten third-party validation that our enzyme technology is equal, may be slightly better than all competitive enzyme products that are available for biomass commercial to-date. So it’s got a good position and we’ve been received warmly accordingly. I think that answers two of the questions. This is a corporate priority, Patrick, to really put a clear commercialization pathway in place for a company and, obviously, for investors. I would be hopeful that within the next couple of quarters we will be providing our investor base with milestones according to that goal. Patrick Jobin – Credit Suisse: Okay. And just last question and then I’ll hop back in queue, but I guess more on the financial side, if we take your color on the gross margin under the new Arch agreement and I guess that’s about half of the product revenue or a little bit around that, would you expect that type of gross margin to continue? And then are you expecting more on-patent revenue in 2013, so should we expect that gross margin to increase for that side of their portfolio?

The on-patent, the outlook for growth in 2013 versus 2012 on on-patent is up and up more strongly than it would be expected in the generic side. So we should have an improving mix of on-patent versus generic. And then you heard David O’Toole provide you with some details about the improved margin outlook of the large atorvastatin enzyme business versus the past. So, clearly both fundamentals bode well for increased margins 2013 versus 2012 in our pharmaceutical products and services business. Patrick Jobin – Credit Suisse: Great, thanks.

Welcome.

Your next question is coming from the line of Chris Kovacs from Baird. Patrick Jobin – Credit Suisse: Chris Kovacs – Robert W Baird: Hi guys. Thanks for taking my question. Just want to start out the news earlier last month that Raízen had selected Iogen, worked with them on a plant, just want to get your reaction there, how you feel it leaves in terms of position with Raízen?

We received the public announcement that Raízen was working with Iogen to further advance the process technology for second generation ethanol. We took that as good news. It’s a good public sign of progress from Raízen. But, however, Raízen is yet to make a firm corporate public commitment to build second generation ethanol capacity in Brazil, although we know they are studying and the indication of working with Iogen supports the fact that it is serious agenda for Raízen. So they track their pathway for investing in second generation ethanol. It has been slower frankly than we would have expected for them to come forward with their investment plans. Obviously, as our leading shareholder and a key partner for Codexis, we’ve been working with them very closely. We gave some color in the script that those discussions have led to us not expecting any R&D funding, however, we still work closely with them as a potential prospect for buying CodeXyme enzymes as we commercialize them in the future. Chris Kovacs – Robert W Baird: Okay, thanks. And then just a follow up. Obviously, you talked about focusing on cost reductions I think in Q3. As we look into Q4 and then into 2013, I mean how much realistically do you, are you targeting I think you can take out of the SG&A and R&D lines, where do you want that to be optimally?

Maybe I’ll ask David to respond to that question. David O’Toole: Yeah, I mean we’re still working through our 2013 plan. We’ve already done the major restructuring in 2013. We still are focused on taking out as you indicated some SG&A costs that we want to reduce. In the previous call, we indicated that we want to target a cash burn in the low 1 million part and the 1 million digit, less than 1 million I guess is what I am trying to say and I think that’s still our target is that we want to get our expenses in line with the revenue that we are going to be generating next year. Chris Kovacs – Robert W Baird: Great, thanks, guys.

Thank you.

Your next question is coming from the line of Mike Ritzenthaler from Piper Jaffray. Mike Ritzenthaler – Piper Jaffray: Hi. Good afternoon. So just a couple of questions about the revenues. So we have been expecting the $7.5 million kind of cleanup from the Shell arrangement but obviously the collaboration revenues were a lot higher. Was there anything unusual in that upside that happened with that cleanup? David O’Toole: No, there wasn’t. The only one as you indicated was the $7.5 million of collaboration from Shell that was the cleanup. Mike Ritzenthaler – Piper Jaffray: Okay. And would you mind breaking down between FTEs and milestone payments and I guess, is it safe to assume that that cleanup is done? David O’Toole: That clean up is done... Mike Ritzenthaler – Piper Jaffray: Okay. David O’Toole: At this point as of the end of the third quarter. We have not received the payment but that’s sitting on our balance sheet and that will be collected in the fourth quarter.

Mike, I would add, this is John. I would add that the milestone portion of the $7.5 million was a minority of that $7.5 million. Mike Ritzenthaler – Piper Jaffray: Okay, fair enough. Then on income tax, the startup mid next year, what’s the early read from the pilot facility and any sort of sampling that you’ve done from Redwood Falls?

Okay, the early read is the construction is on progress. We have pictures of vessels being put in place. So on a construction project point of view, timeline is going well, which continues to at least set the outlook of middle of next year after the startup. The microorganism productivity development is going well. We’ve made good progress. Even through the downsizing exercise, team’s done some nice improvements in the productivity of the organism. We have sampled very small scale samples from the R&D effort in Redwood City and most of our R&D attention is focused on improving the yields from the organism as opposed to improving the specification of the detergent alcohol being produced. Mike Ritzenthaler – Piper Jaffray: Okay. And then on the Arch just one last one from me on the Arch agreement. So, if I understood the comments right and I’m sorry there was a little bit of a breakup in the line for some reason, but I just wanted to make sure I understood that it’s more of a focus on the enzyme part as opposed to the previous arrangement that had some other sort of overhead that you were responsible for, is that true, that’s subscribing the 55% in the last nine months versus the 5%?

Yeah. Let me start, David please jump in. David O’Toole: Yeah.

That’s correct. Prior, Codexis was responsible not only for providing the enzyme to make the intermediate, but also was responsible for the manufacturing of the intermediate or actually more precisely... Mike Ritzenthaler – Piper Jaffray: Okay.

Having the intermediate be manufactured for us. But then we took responsibility for owning that intermediate and selling and serving the customer with that intermediate. So those are substantially a more complex role for Codexis in the supply chain of atorvastatin. And then as we advanced our collaboration with Arch Pharmalabs, it became clear that there was a streamlining of that operation that could benefit both Arch and Codexis by having Codexis just focus on supplying and optimizing in terms of the application and leave other elements of the supply chain that we used to manage to be managed by Arch going forward. Mike Ritzenthaler – Piper Jaffray: All right, that makes sense. Okay, thanks guys.

(Operator Instructions). Our next question comes from the line of Stacey Hudson from Raymond James. Stacey Hudson – Raymond James: Hi, good afternoon, guys. David O’Toole: Good afternoon. Stacey Hudson – Raymond James: Just want to follow up on Patrick’s question. You mentioned on the 2Q call that CodeXyme sales outside of Raízen were likely a 2015 type of event. Given the conversations that you’re having, do you still maintain that view?

I’m sorry. For some reasons I couldn’t hear your question fully. Stacey, can you just rephrase it? I apologize. Stacey Hudson – Raymond James: Sure, no problem, sorry. On the 2Q call, you mentioned that you didn’t expect CodeXyme sales outside of Raízen should happen until like 2015, do you still kind of use that timeline as something that’s reasonable or do you see it maybe moving forward with the conversations that you’re having?

Yeah, I think that the outlook for 2015 is still a reasonable outlook. Practically, we haven’t been able to engage in any third-party discussions outside of Shell and Raízen until very, very recently. So it’s very early days for really building these new potential partnerships for CodeXyme. So we’ll have timeline to build those partnerships to craft them in a way that works for Codexis and our partner. And then to start to continue the development of the enzymes to ensure we stay ahead of our competition for these enzymes and then, of course, the build out of the enzyme factories in connection with ethanol producers building their second generation ethanol plant. So if you put some practical timeline elements on it, we definitely into 2015, maybe 2016 before we start to see revenue from enzymes sales for CodeXyme. Stacey Hudson – Raymond James: Okay, thank you. And then on CodeXol, what do you think the timeline would be for finding commercialization partners for that?

Finding commercialization partners or generating revenue? Stacey Hudson – Raymond James: Announcing something as far as commercialization partners?

Yeah, I think that prospect of announcing a commercialization partner before we do the pilot run in the middle of next year is a bit low. It’s possible but I wouldn’t set your expectation that we’re going to strike a commercialization, a public commercialization deal in CodeXol prior to us running the organism through the demo scale facility in Italy, and that’s the way we’re expecting the commercialization path to follow. Stacey Hudson – Raymond James: Okay.

And to show that scale and then be in a better position to strike a commercialization deal. Stacey Hudson – Raymond James: All right, sure. Thank you.

Welcome.

And at this time, I’m showing no further questions in queue. I would like to turn the call back over to Mr. John Nicols for any closing remark.

Okay. Well, thank you very much everybody for joining our call, and we look forward to continuing to update you as we progress our company going forward. Thank you very much again.

Ladies and gentlemen, this does conclude today’s presentation. Thank you once again for your participation. You may now disconnect. Have a great day.