Category Archives: Databases

The Coronavirus Antibody Database: 10 months on, 10x the data!

Back in May 2020, we released the Coronavirus Antibody Database (‘CoV-AbDab’) to capture molecular information on existing coronavirus-binding antibodies, and to track what we anticipated would be a boon of data on antibodies able to bind SARS-CoV-2. At the time, we had found around 300 relevant antibody sequences and a handful of solved crystal structures, most of which were characterised shortly after the SARS-CoV epidemic of 2003. We had no idea just how many SARS-CoV-2 binding antibody sequences would come to be released into the public domain…

10 months later (2nd March 2021), we now have tracked 2,673 coronavirus-binding antibodies, ~95% with full Fv sequence information and ~5% with solved structures. These datapoints originate from 100s of independent studies reported in either the academic literature or patent filings.

The entire contents CoV-AbDab database as of 2nd March 2021.
Continue reading →

Curious About the Origins of Computerized Molecules? Free Webinar Dec 22…

After the stunning announcement at CASP14 that DeepMind’s AlphaFold 2 had successfully predicted the structures of proteins from their sequence alone, it’s hard to believe we began this journey by representing molecules with punched cards…

Image of a punched card, showing 80 columns and 12 rows, with particular rectangular holes representing the 1 bits of binary numbers. The upper right corner is cut at an angle, to facilitate feeding the card into a punched card reader. The column numbers are printed along the bottom. The words “IBM UNITED KINGDOM LIMITED” are printed along the very bottom. This card is line 12 from a Fortran program, “12 PIFRA=(A(JB,37)-A(JB,99))/A(JB,47) PUX 0430”. Image Credit: Pete Birkinshaw, Manchester, U.K. CC BY 2.0

Tales of carrying stacks of punched cards to the computer centre with a line drawn diagonally on the side of the stack, to help put them back in order should you trip and fall—seem like another universe—but this is what passed for the human-computer interface in much of the mid-20th century.

Continue reading →

BioDataScience101: a fantastic initiative to learn bioinformatics and data science

Last Wednesday, I was fortunate enough to be invited as a guest lecturer to the 3rd BioDataScience101 workshop, an initiative spearheaded by Paolo Marcatili, Professor of Bioinformatics at the Technical University of Denmark (DTU). This session, on amino acid sequence analysis applied to both proteomics and antibody drug discovery, was designed and organised by OPIG’s very own Tobias Olsen.

Continue reading →

Speaking about Sequence and Structure at a Summit

A couple of weeks ago I was lucky enough to be asked to speak at the 5th Computational Drug Discovery & Development for Biologics Summit. This was my first virtual conference – it was a shame I didn’t get to visit Boston, and presenting to my empty room was slightly bizarre, but it was great to hear what people have been working on, and there’s definitely something to be said for attending a conference in fluffy socks…

A, antibody structure. An antibody is made up of four chains: two light (orange) and two heavy (blue). Each chain is made up of a series of domains—the variable domains of the light and heavy chains together are known as the Fv region (shown on the right; PDB entry 12E8). The Fv features six loops known as complementarity determining regions or CDRs (shown in dark blue); these are mainly responsible for antigen binding. B, example sequences for the VH and VL, highlighting the CDR regions and the genetic composition. It is estimated that the human antibody repertoire contains up to 1013 unique sequences, enabling the immune system to respond to almost any antigen. This is possible through the recombination of V, D and J gene segments, junctional diversification, and somatic hypermutation.
Continue reading →