Collaborative Drug Discovery (CDD)
Transforming Data Management in Drug Discovery

Dr. Barry A. Bunin, CEO and President

Drug discovery operates across laboratories, clinical trials, and computational models, generating an immense volume of data on everything from genetic information to chemical compounds, clinical outcomes, and preclinical results.

The challenge is not just gathering data but structuring, analyzing, and storing it in a way that ensures accessibility and interpretability for researchers, developers, and decision-makers. While managing this data is intricate and demanding, Collaborative Drug Discovery’s (CDD) solution simplifies the process, offering a streamlined and efficient approach to overcoming these complexities.

A Silicon Valley-based company, CDD has created CDD Vault, a web-based solution designed to streamline chemical and biological data management across the entire drug discovery process. An essential part of the platform is CDD Vault’s Electronic Laboratory Notebook (ELN), which enables scientists to capture experimental procedures, observations, and results in the same secure environment where chemical and biological data are managed and shared. The platform enables drug discovery teams to manage and analyze data from multiple disciplines within a single, secure, easy-to-use system and has garnered the trust of researchers, scientists, and companies around the globe.

Dr. Barry A. Bunin, CEO and President, leads the company with a strong vision rooted in his deep understanding of the challenges faced by researchers in the field. He notes, “Our platform continues to empower researchers to make more informed, data-driven decisions in drug discovery.”

Pioneering a New Era in Scientific Data Management

How did CDD Vault evolve as a web-first solution for scientific data management?

When Dr. Bunin founded CDD, the vision was clear: to create a solution that would streamline data management in drug discovery by simplifying complexity. The goal was to enable researchers to handle large volumes of chemical and biological data with ease while ensuring secure collaboration across teams and organizations. From the very beginning, CDD Vault was conceived as a web-first solution, long before cloud computing became mainstream.

“One of the key differentiators for CDD Vault is that it is not just about managing data; it is about making the data work for you. The platform simplifies complexity so researchers can focus on discovery rather than getting bogged down in the intricacies of data management,” says Dr. Bunin. “Our tagline, ‘Complexity Simplified,’ reflects this philosophy because we have built a system that does all the heavy lifting so you do not have to.”

CDD Vault was one of the first hosted systems to come to market, even before cloud computing platforms such as AWS gained widespread adoption. By offering a cloud-based solution, CDD Vault has enabled research teams to collaborate across geographies with high levels of security and efficiency. With servers in both North America and Europe, 99.9 percent uptime, and a flawless security track record, the platform ensures that sensitive data remains protected while providing researchers with the tools they need to accelerate their work.

Simplifying Collaboration Across Teams and Companies

How does CDD Vault enable secure collaboration across teams, partners, and organizations?

One of the core principles Dr. Bunin emphasized during the development of CDD Vault was collaboration. Drug discovery is rarely a solo endeavor; it involves teams of scientists, researchers, and clinicians from different disciplines working together to solve complex problems. Whether it is a chemist working alongside a biologist or a biotech firm collaborating with a large pharmaceutical company, seamless communication and data sharing are essential.

"Our platform continues to empower researchers to make more informed, data-driven decisions in drug discovery."

“One of the things we hear from customers all the time is that CDD Vault makes collaboration much easier. Whether you are working with different teams within the same company or with external partners such as CROs, large pharmaceutical companies, or academic institutions, the platform ensures data is shared securely and that all stakeholders remain aligned,” Dr. Bunin explains.

The ability to collaborate securely across companies and disciplines has made CDD Vault valuable to organizations ranging from startups to large pharmaceutical companies. This capability also delivers meaningful economic advantages. Rather than placing dedicated personnel on-site for weeks or months, companies can onboard new teams or external partners quickly through online meetings and training sessions, saving both time and money.

Security remains a top priority, and CDD Vault was designed with the principle of secure collaboration in mind. The platform’s architecture enables precise data partitioning, ensuring that sensitive data is accessible only to authorized users, whether inside or outside the organization. This level of security has been critical in building trust, particularly in an industry where confidentiality and regulatory compliance are paramount.

What capabilities allow CDD Vault to manage chemical and biological data with precision?

Another key feature that distinguishes CDD Vault from its competitors is its ability to handle data at the atomic level. Drug discovery is a highly complex process that requires researchers to manage not only the chemical structure of compounds but also their biological activity and potential toxicity. CDD Vault excels at managing both chemical and biological data, ensuring that every atom in a compound is tracked with precision. This level of accuracy is especially important when working with biologics or small molecules, where slight changes in molecular structure can significantly affect efficacy and safety.

Dr. Bunin is particularly proud of the platform’s ability to manage chemically aware biologics, such as antibody-drug conjugates (ADCs). These drugs, which combine small molecules with biologics, are especially difficult to model and track due to their complex molecular structures. “With CDD Vault, we track every atom, every bond, and every modification in these biologic systems,” he says. “This precision gives researchers the confidence to move forward in the discovery process, knowing the data they are using is accurate and reliable.”

The platform also allows researchers to easily visualize bioactivity data, including IC50 curves and microtiter plate assays, and identify patterns within their datasets. For biologists working in the lab, this capability can save hours of manual analysis and reduce the risk of human error. With CDD Vault, scientists can focus on interpreting results rather than worrying about data integrity or calculation errors.

In recent years, AI and machine learning have played an increasingly significant role in drug discovery, and CDD has actively embraced this shift. One of the most notable developments in CDD Vault is its AI-powered module, which enables the generation of new molecular structures, known as bioisosteres, that are both chemically feasible and scientifically valuable.

“We have developed a system that allows researchers to generate new ideas based on the data already in the platform, whether they are working with small molecules or biologics,” says Dr. Bunin.

These AI-generated bioisosteres are not merely theoretical. They are practical, real-world alternatives that medicinal chemists can use to optimize drug candidates. This capability ensures that CDD Vault functions not only as a data management platform but also as a source of new intellectual property. Researchers can generate novel compounds, evaluate patent status, and explore potential synthetic routes within the same system.

The AI capabilities of CDD Vault are grounded in sound scientific principles. Unlike AI systems that generate theoretical molecules without regard for chemical feasibility, CDD Vault ensures that generated bioisosteres are realistic and likely to be synthetically viable. This distinction is critical in a field where many AI tools produce vast numbers of impractical candidates.

Bringing Precision to Data Analysis

Another area where CDD Vault excels is assay informatics. Assays are a critical component of drug discovery, and meaningful comparison across assays is essential to understanding drug candidate effects. Historically, assay comparison has been difficult due to variability in methodologies and instrumentation. CDD Vault addresses this challenge by enabling quantitative assessment of assay similarity, allowing researchers to make direct and meaningful comparisons.

In collaboration with the Pistoia Alliance, CDD Vault developed a patented system for quantifying assay metadata, enabling more precise comparisons. This innovation is particularly valuable for model development and data transfer learning, helping researchers identify the most relevant data for their work. By making assay informatics quantitative, CDD Vault advances drug discovery and helps researchers maximize the value of their data.

The true measure of CDD Vault’s success lies in customer outcomes. One notable example is Medivation, whose use of CDD Vault across three continents supported the development of cancer therapies that ultimately led to a 14 billion dollar acquisition by Pfizer. These and other success stories highlight the platform’s ability to deliver real value, both in data management and in accelerating discovery.

Helping Researchers Turn Data into Discoveries

As CDD looks ahead, Dr. Bunin remains focused on expanding the reach and capabilities of CDD Vault. For the team at CDD, the journey is far from complete. With CDD Vault, the company has established a new standard for scientific data management in drug discovery.

“We are excited about the future,” he says. “There are many new technologies on the horizon, especially in chemically aware biologics and AI-powered drug discovery. Our goal is to continue innovating and provide customers with the tools they need to stay ahead of the curve.”

Over the next 18 to 24 months, CDD plans to increase platform adoption, particularly within the biologics space, where significant growth potential exists. The company is also continuing to enhance its AI capabilities, enabling more advanced data analysis and decision-making. As drug discovery continues to evolve, CDD Vault is well positioned to remain at the forefront, helping researchers turn data into discoveries that could change the world.