Free advice for SMEs on how computational chemistry can advance your project
Through our partnership with the Medicines Discovery Catapult we are offering a limited number of computational chemistry consultancy sessions to ...
Academia and industry always have a lot to gain from cultivating close ties with each other. As with any relationship, getting the balance right between give and take starts with a generous attitude from both parties.
Cresset develops software and services for small molecule discovery and design, primarily for the pharmaceutical R&D. We work with the global academic community in a number of ways, including collaborative projects, Knowledge Transfer Partnerships and commercialization of academic methods. We also invest in academic programs with the hope of shared benefits on several different timescales.
Cresset’s software gives new insight to projects I’ve been working on for the past three to four years. I specifically use it to see how proteins, DNA and molecules interact and bind to each other. If we can design drug molecules that will bind to DNA the same way proteins do, we can open up whole new lines of therapy. Cresset is supportive of academic research and they’ve been wonderful to work with to get everything up and running.
Dr Daniel Barr, Assistant Professor of Biochemistry, Department of Chemistry and Biochemistry, Utica College, USA
We wholeheartedly believe that our methods shorten the path to new compounds. That by using Cresset computational software, more and better compounds will be discovered more efficiently. Therefore, we want to spread the word to the next generation of computational chemists, who are already far more computationally literate than any previous generation. We are actively involved in teaching and training the next generation of computational chemists.Here’s what we’re doing to support that goal:
By being closely associated with the up and coming generation of computational chemists, we’re also staying in touch with how our user base is growing and changing.
The traditional gap between medicinal chemists and computational chemists is becoming blurred. It is unthinkable that today’s medicinal chemist graduates will not use computers in their every-day work. They may not want to work with command line code, but they feel very at home with our chemistry software.
In response, we’re changing how we develop new tools in order to make them more accessible to a widening group of users. We continue to invest heavily in usability and good design, and we also continually review and add new tools that support workflow.
Everyone who works in computational chemistry knows that the open source community develops many and varied methods, most of which are useful and some of which are outstanding.
Rather than viewing this as competition for commercial software, we see it as an opportunity for partnership. Rather than developing new methods, we can work with academics to build their excellent code into our computational chemistry environments.
But why would anyone pay for an open source method?
The answer is convenience, usability, validation and support. Some professionals working in industry find it difficult to adopt academic methods for their work since they’re not supported by their in-house IT policies. We put academic methods into a professional environment with a highly usable GUI and make sure it integrates with the rest of our software and complies with other protocols. We also offer a professional level of support.
In return, the academic authors may receive royalties, additional kudos from broader usage of their code, valuable links with industrial scientists, plus a broader user community contributes to the ongoing development of their methods.
For example, WaterSwap is a widely used, open source method implemented in SIRE. It was developed by Dr Chris Woods at the University of Bristol. Cresset collaborated with Dr Woods to license WaterSwap and include it in Flare, our structure-based design application.
Figure 1: WaterSwap is a thermodynamic integration method for investigating ligand-protein energetics. Green residues show where the ligand is gaining the most energy from interaction. Red residues show where water binding is preferred and represents opportunities to improve ligand design.
Visualizing the inhibitor/substrate binding site of protein crystal structure in Cresset using field points calculated by XED force field is very informative. The protocols for all the modules in Cresset are very quick and easy to use. Forge and Spark are excellent programs for LBDD. The radial plots obtained from alignment methods implemented in Forge provide a visual inspection of results and could be effectively used for simultaneously comparing any number of physical properties for the compounds in the dataset. I strongly believe that Cresset software is an important inclusion in the spectrum of software programs used for Computer Aided Drug Discovery paradigm.
Dr. Prija Ponnan, Department of Chemistry, University of Delhi
One of the hurdles faced by many software vendors in validating their methods is the understandably high level of confidentiality associated with pharmaceutical R&D. To take one (anonymized) example. Two years ago Blaze, our virtual screening platform, was used to successfully identify a potential hit from the large compound libraries of a major organization. That compound is now going into clinical trials. However, the time scales are such that it could be ten years before anything is ever published about the methods used to discover the compound.
By contrast, academic groups using our software are extremely likely to report their results in papers, thus creating a healthy supply of citations. Our customers need proof that our software delivers results, and academia is an ideal source.
We offer significant reductions on software used for academic research, and we offer flexible licensing options for software used for teaching or PhD research.
Finally, we want to hear from opinion makers, and this can be the most mutually valuable exchange of all.
Our software needs to provide outstanding science and support changing workflows. As we develop and improve applications we need to keep listening to researchers about how they are working and what will help them stay on leading edge of research. Close relationships, sometimes over many years, encourages an open dialog that helps us to get our products right, and helps leading academics to get the software that will be of most use to them most in their research.
We want academics to be able to work as efficiently as possible to find compounds that will help in therapeutic areas of need. And we also want to provide the best possible tools to the broader market.
See the licensing options for our ligand-based and structure-based applications. Or contact us for a free confidential discussion to find out how Cresset Discovery Services experts can add value to your project.