Blog CSD

As the size of the Cambridge Structural Database (CSD) has just passed one million structures, it seems an appropriate time to look at some of the applications of this ever-growing resource. Whilst the CSD is certainly useful as a central record of past data collections, perhaps the more significant benefits are the insights that can be gained from looking at this mass of data as a whole. In this blog, I’ll show some examples of what can be discovered from statistics generated from the CSD when looking at drug-like compounds. A paper written by CCDC colleagues with researchers from Pfizer and AstraZeneca (Journal of Pharmaceutical Sciences, Volume 108, Issue 5, 2019, Pages 1655-1662, https://doi.org/10.1016/j.xphs.2018.12.011) gives an in-depth statistical analysis of drug compounds in the CSD.

Today marks a huge milestone in structural chemistry – the sharing of one million organic and metal-organic crystal structures, an achievement of which the entire community should be extremely proud! The creation of the Cambridge Structural Database (CSD) to share and distribute these structures is truly a team effort. Crystallographers worldwide deposit their data with us and our team of Deposition Coordinators and Scientific Editors here in Cambridge curate and enhance their structures into the database.

We are pleased to announce the latest update of the CSD software including enhanced protein handling features throughout the CSD portfolio and greatly improved searching capabilities in the CSD Python API.

Did you know that every year we generate a range of annual statistics based on the Cambridge Structural Database (CSD)?  These allow us to see how the CSD is evolving and provide some insights into the direction small molecule structural chemistry is headed.

In recent years, CSD Communications has grown to be one of the most popular methods for publishing structural data among the crystallographic community with more than 15,000 CSD Communications published in the last 5 years and 28,000 published overall since the 1980s. This represents a formidable amount of structural data which without CSD Communications may never have been made available to the scientific community. To promote the benefits which this wealth of crystallographic data can offer to the research community, the CCDC has therefore recently been working to make CSD Communications more convenient to publish, access and cite.

Data integrity investigations at the CCDC 

The integrity of the data within the Cambridge Structural Database (CSD) is of great importance to the CCDC and, no doubt, to the many scientists across the world that use the CSD as part of their research. The CSD is a trusted repository of crystallographic data and as such we are taking a pro-active approach to ensuring the data that we store is both trustworthy and consistent, enabling scientists to find and utilise the best data for their research. Our overall aim is to be able to help depositors, peer reviewers and wider users of the CSD identify the quality and integrity of the data and to ensure, as far as possible, that there are no cases of fraud or plagiarism within the CSD.

In a recent blog - CSD Data Curation - The Human Touch -  we’ve described the work that goes on when new structures are added to the Cambridge Structural Database (CSD). However, It’s important to realise that this isn’t the end of the story -  as we get close to adding the one millionth structure to the CSD, it seems like an appropriate time to describe some of the processes we undertake at the CCDC to ensure that the data we make available to scientists continues to empower and inform their research long after it’s initial deposition.

Today is International Women’s Day (IWD - #InternationalWomensDay), celebrated each year on the 8^th of March, so what better day to recognise some of the many inspiring women in the field of crystallography.

The beginnings of International Women’s Day started in 1909/1910 but it wasn’t until 1975 that it was adopted by the United Nations. Today IWD is celebrated in many countries worldwide and is even a public holiday for some. IWD can mean different things to different people, for some it is a chance to call for change and improve gender equality, for others it is the perfect opportunity to highlight the achievements of women in their fields and try to inspire a new generation.

Rather than tell you how long I have worked at CCDC as a Scientific Editor in the Database Group, perhaps I will instead measure the time in the growth of the Cambridge Structural Database (CSD) and tell you that when I started working here, the CSD had just passed the 180,000 mark. As I’m sure you know, today, more than 800,000 structures later, we are very close to entering the 1 millionth structure into the CSD.

But what do we mean when we say ‘entering’ data into the CSD, a process we refer to as data curation?

Later this year the world of structural chemistry will reach a tremendous milestone, the sharing of one million organic and metal-organic structures through the Cambridge Structural Database (CSD). The CSD was one of the first numerical scientific databases to be established and today enables scientists and educators in over 70 countries to learn from the data.