Modelling β−Trefoil Proteins Using an Object-Oriented Database

نویسندگان

  • Antonis I. Koussounadis
  • David W. Ritchie
  • Chris J. Secombes
چکیده

This article describes on-going work using an object-oriented database, P/FDM, to build 3D homology models of β-trefoil proteins such as Interleukin-1 (IL-1), by exploiting existing structural data from known structures of the same fold. The model-building procedure is based on the powerful querying capabilities of P/FDM that allows data access, navigation, and computation to be mixed freely and easily in order to formulate complex structural queries. The database can be queried using a Java-based graphical user interface. Using the P/FDM β−trefoil database, the above approach allows to “cut-and-paste” fragments from existing β−trefoil structures to build the model. The structural part of the database contains objects for the description of proteins, as well as β-trefoil structure-specific entities. Data are organised according to a global β-trefoil structural alignment based on superposition of the 18 core residues of the fold, identified from previous structural studies. The database is currently populated with 46 trefoil domains and further structures are being added in order to make available a richer collection of “spare parts” for modelling. Future enhancements such as improved side chain placement and fragment clustering are also described.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Object-oriented Database Design: What Is the Diierence with Relational Database Design?

Object-oriented database design is not only a simple extension of relational database design. By modelling structure as well as behaviour of real world entities as coherent units, object-oriented database design succeeds in capturing more semantics of applications already in the design phase. The use of object-oriented concepts like inheritance allows an adequate modelling and a better applicat...

متن کامل

Object-oriented modelling with viewpoints

Proposed object-oriented approaches are still in an initial stage of investigation and are mainly limited to modelling CAD applications which manipulate ill-deened, evolving and multifaceted objects. In this paper , we argue in favour of a model, called CEDAR, which aims at easing the modelling process by endowing object-oriented approach with a viewpoint notion. keywords: object-oriented datab...

متن کامل

Mixing Classes and Prototypes: An Object Oriented Approach to Semantic Image modelling

Classical object oriented database management systems fail in semantic modelling of images, because such objects are not easily de nable in terms of conceptual structures (classes, database schemes, ...). Besides, object-oriented languages have evolved in various directions, including but not limited to class-based languages. Prototype-based languages represent a serious alternative to class-ba...

متن کامل

Modelling for Spatial Databases

Data modelling is a critical stage of database design. Recent research has focused upon object-oriented data modes, which appear more appropriate for certain applications than either the traditional relational model or the entity-relationship approach. The object-oriented approach has proved to be especially fruitful in application areas, such as the design of geographical information systems w...

متن کامل

Visualising Data Modelling Constructs in an Object-oriented Database

Object-oriented databases are seen as potential successors to rela-tional databases, at least in part because they provide a richer set of data modelling constructs. This paper addresses the challenge to interface designers posed by such constructs to support data browsing and modelling through powerful and perspicuous visualisations, with the additional requirement that the visualisations shou...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2004