CLP-based protein fragment assembly

The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a database of known protein structures that clusters and classifies the fragments according to similarity and frequency. The problem of assembling fragments into a complete conformation is mapped to a constraint solving problem and solved using CLP. The constraint-based model uses a medium discretization degree Ca-side chain centroid protein model that offers efficiency and a good approximation for space filling. The approach adapts existing energy models to the protein representation used and applies a large neighboring search strategy. The results shows the feasibility and efficiency of the method. The declarative nature of the solution allows to include future extensions, e.g., different size fragments for better accuracy.Comment: special issue dedicated to ICLP 201

Constraint Logic Programming approach to protein structure prediction

BACKGROUND: The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems. RESULTS: Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known) secondary structure and the presence of disulfide bridges are used as constraints. Simplified structures obtained in this way have been converted to all atom models with plausible structure. Results have been compared with a similar approach using a well-established technique as molecular dynamics. CONCLUSIONS: The results obtained on small proteins show that Constraint Logic Programming techniques can be employed for studying protein simplified models, which can be converted into realistic all atom models. The advantage of Constraint Logic Programming over other, much more explored, methodologies, resides in the rapid software prototyping, in the easy way of encoding heuristics, and in exploiting all the advances made in this research area, e.g. in constraint propagation and its use for pruning the huge search space

Discharge hydrograph estimation at upstream-ungauged sections by coupling a Bayesian methodology and a 2-D GPU shallow water model

Abstract. This paper presents a novel methodology for estimating the unknown discharge hydrograph at the entrance of a river reach when no information is available. The methodology couples an optimization procedure based on the Bayesian geostatistical approach (BGA) with a forward self-developed 2-D hydraulic model. In order to accurately describe the flow propagation in real rivers characterized by large floodable areas, the forward model solves the 2-D shallow water equations (SWEs) by means of a finite volume explicit shock-capturing algorithm. The two-dimensional SWE code exploits the computational power of graphics processing units (GPUs), achieving a ratio of physical to computational time of up to 1000. With the aim of enhancing the computational efficiency of the inverse estimation, the Bayesian technique is parallelized, developing a procedure based on the Secure Shell (SSH) protocol that allows one to take advantage of remote high-performance computing clusters (including those available on the Cloud) equipped with GPUs. The capability of the methodology is assessed by estimating irregular and synthetic inflow hydrographs in real river reaches, also taking into account the presence of downstream corrupted observations. Finally, the procedure is applied to reconstruct a real flood wave in a river reach located in northern Italy