When considering the prediction of a structural class for a protein as a classification problem, usually a classifier is based on a feature vector x ∈ R, where the features represent certain attributes of the primary sequence or derived properties (e.g., the predicted secondary structure) of a given protein. Since the structure of a protein (i.e., its native conformation) is stable only under s...

The paper uses the SCOP theory of concepts to model the role of environmental context on three levels of entrepreneurial opportunity: idea generation, idea development, and entrepreneurial decision. The role of contextual-fit in the generation and development of ideas is modeled as the collapse of their superposition state into one of the potential states that composes this superposition. The p...

Digital Terrain Models (DTM) are topic of this paper. The SCOP approach uses hybrid DTMs which combines grid based and triangulated terrain models. A detailed discussion on interpolation and filter methods will be made as they can be employed, for example, to derive DTMs from laser scanning data. Additionally the database of SCOP and the integration into third-party software will be presented. ...

Classification and prediction of protein structure has been a central research theme in structural bioinformatics. Due to the imbalanced distribution of proteins over multi SCOP classification, most discriminative machine learning suffers the well-known ‘False Positives’ problem when learning over these types of problems. We have devised eKISS, an ensemble machine learning specifically designed...

The Structural Classification of Proteins (SCOP) database has facilitated the development of many tools and algorithms and it has been successfully used in protein structure prediction and large-scale genome annotations. During the development of SCOP, numerous exceptions were found to topological rules, along with complex evolutionary scenarios and peculiarities in proteins including the abili...

PROCOGNATE is a database of protein cognate ligands for the domains in enzyme structures as described by CATH, SCOP and Pfam, and is available as an interactive website or a flat file. This article gives an overview of the database and its generation and presents a new website front end, as well as recent increased coverage in our dataset via inclusion of Pfam domains. We also describe navigati...

This article presents a historical review of the protein structure classification database CATH. Together with the SCOP database, CATH remains comprehensive and reasonably up-to-date with the now more than 100,000 protein structures in the PDB. We review the expansion of the CATH and SCOP resources to capture predicted domain structures in the genome sequence data and to provide information on ...