DockIt: Development and launch of a crowd-sourced serious-games platform for protein docking for use by the public and the scientific community.

AIM - The aim of this grant is to develop a serious and enjoyable computer game (DockIt) used by numerous players (a crowd) to model how two large biological molecules (proteins) fit together and thereby perform their function. PROTEIN DOCKING: AN UNSOLVED BIOLOGICAL PROBLEM - Proteins are large biological molecules, generally with at least 1,000 atoms, which perform many biological functions. The three-dimensional structure of a protein is complex. Central to its biological activity is that often it docks to another protein to form a complex. The structure of the complex is dictated by how the atoms in the molecules interact with each other. The shape of the complex helps in understanding the mechanism of action of proteins and this knowledge can have major benefits in food security, industrial biotechnology and the design of novel pharmaceuticals. Computational approaches are used to predict the shape of a complex given knowledge of the structures of the unbound components. However the programs have only limited success. Research in other areas of science, including modelling the shape of proteins, has shown that individuals using human judgement can sometimes find solutions to problems that cannot yet be solved automatically. In particular finding consensus solutions from a crowd of players can yield successful results. This approach is known as crowd sourcing. Accordingly, we propose to develop a computer game DockIt where the players will manipulate the two protein structures and predict a complex. This is similar to solving a three-dimensional jigsaw puzzle. The docking will start with a set of possible complexes generated by state of the art programs and thus successful plays can yield predicted structures superior to those automatically generated. THE DOCKIT GAME - We will design DockIt so that it is fun to play by exploiting the latest technology and design from the casual games industry. We will develop DockIt for a range of platforms including tablets, smartphones and PCs thereby ensuring wide take-up. A user will be able to adjust the relative position of the two proteins and to change the shape of each protein. The approaches to alter the proteins will be encoded as a set of recipes which the user can employ. We will provide a scoring function to feedback to the players an estimate of the quality of the predicted structure. RELEASE OF DOCKIT - We will release DockIt for use by the academic community and to the general public. Our strategy to publicise DockIt is to work with our partners, collaborators and industry contacts to promote DockIt via their extensive player databases, for example by inclusion in newsletters. The docking targets will include those for which the solution is known and those where DockIt is used to solve a real-world biological problem. Players will download a possible complex from the host server and then change its shape to predict the best complex which will then be returned to the server. Results from different players will be pooled and we will identify the best prediction. Players will be supported by the presence of a tutorial which will provide progressive steps to learn the game. There will be E-mail support and a social network group will be established (e.g. Google+, FaceBook, LinkedIn and Twitter). DISSEMINATION - DockIt will be disseminated to the scientific community and the general public. We will make presentations at scientific conferences and publish technical papers. We will issue a press release aimed at the games together with popular science magazines. We will also target TV, Radio, the educational press and trade bodies. We envisage that DockIt could be used at schools and universities in teaching.