GOPred: GO Molecular Function Prediction by Combined Classifiers

Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines different methods to better represent protein function. First, we formulated the function annotation problem as a classification problem defined on 300 different Gene Ontology (GO) terms from molecular function aspect. We presented a method to form positive and negative training examples while taking into account the directed acyclic graph (DAG) structure and evidence codes of GO. We applied three different methods and their combinations. Results show that combining different methods improves prediction accuracy in most cases. The proposed method, GOPred, is available as an online computational annotation tool (http://kinaz.fen.bilkent.edu.tr/gopred)

Evaluation of infilled frames: an updated in-plane-stiffness macro-model considering the effects of vertical loads

The influence of masonry infills on the in-plane behaviour of RC framed structures is a central topic in the seismic evaluation and retrofitting of existing buildings. Many models in the literature use an equivalent strut member in order to represent the infill but, among the parameters influencing the equivalent strut behaviour, the effect of vertical loads acting on the frames is recognized but not quantified. Nevertheless a vertical load causes a non-negligible variation in the in-plane behaviour of infilled frames by influencing the effective volume of the infill. This results in a change in the stiffness and strength of the system. This paper presents an equivalent diagonal pin-jointed strut model taking into account the stiffening effect of vertical loads on the infill in the initial state. The in-plane stiffness of a range of infilled frames was evaluated using a finite element model of the frame-infill system and the cross-section of the strut equivalent to the infill was obtained for different levels of vertical loading by imposing the equivalence between the frame containing the infill and the frame containing the diagonal strut. In this way a law for identifying the equivalent strut width depending on the geometrical and mechanical characteristics of the infilled frame was generalized to consider the influence of vertical loads for use in the practical applications. The strategy presented, limited to the initial stiffness of infilled frames, is preparatory to the definition of complete non-linear cyclic laws for the equivalent strut