A Constraint Solver for Flexible Protein Models

This paper proposes the formalization and implementation of a novel class of constraints aimed at modeling problems related to placement of multi-body systems in the 3-dimensional space. Each multi-body is a system composed of body elements, connected by joint relationships and constrained by geometric properties. The emphasis of this investigation is the use of multi-body systems to model native conformations of protein structures---where each body represents an entity of the protein (e.g., an amino acid, a small peptide) and the geometric constraints are related to the spatial properties of the composing atoms. The paper explores the use of the proposed class of constraints to support a variety of different structural analysis of proteins, such as loop modeling and structure prediction. The declarative nature of a constraint-based encoding provides elaboration tolerance and the ability to make use of any additional knowledge in the analysis studies. The filtering capabilities of the proposed constraints also allow to control the number of representative solutions that are withdrawn from the conformational space of the protein, by means of criteria driven by uniform distribution sampling principles. In this scenario it is possible to select the desired degree of precision and/or number of solutions. The filtering component automatically excludes configurations that violate the spatial and geometric properties of the composing multi-body system. The paper illustrates the implementation of a constraint solver based on the multi-body perspective and its empirical evaluation on protein structure analysis problems

25 Years of Applications of Logic Programming in Italy

We present a review of practical applications of Logic Programming appeared in Italy since 1985. We classify them according to their area of application and discuss some trends emerged in the latest developments. Notwithstanding this survey is far to be comprehensive, it shows that Logic Programming successfully evolved and quickly adapted to new challenges offered by a notable variety of application areas

Protein Folding Simulation in CCP

A protein is a list of linked units called aminoacids. There are 20 different kinds of aminoacids and the typical length of a protein is 100\u2013500 units. The Protein Structure Prediction Problem (PSP) is the problem of predicting the 3D native conformation of a protein, when its aminoacid sequence is known. The process for reaching ... n this work we adopt a simplified representation of a protein where each aminoacid is represented by a center of interaction. This simplification, while loosing some details, has the advantage of being computationally tractable and of having smoother potential landscapes. A recently developed empirical contact energy function ..

Exploiting unexploited computing resources for computational logics

Every new desktop or laptop come equipped with a multicore, programmable graphic processing unit (GPU). The computation power of this kind of unit is fully exploited by some graphical software but GPU is mostly idle during common PC use. Moreover, extra GPUs can be added at a very low price per processor. Such kind of parallelism has been recently exploited by some applications able to split the work into small parallel threads. In this paper we investigate the capabilities of this hardware for search problems, where large threads sometimes need to be delegated to each parallel processors. In particular we deal with the well-known SAT problem and focus on NVIDIA CUDA architecture, one of the most popular platforms for GPU. We experimented several implementing choices and evaluated the results. The most interesting outcome is that with the built-in GPU of a typical office desktop configuration we can reach speed-up of one or even two orders of magnitude

Protein C concentrate to restore physiological values in adult septic patients

To describe the efficacy and safety of protein C (PC) concentrate to restore physio- logical values in adult septic patients having clinical contraindications to activated PC. Design: Case series (pilot study). Setting: Three adult ICUs of a University Hospital. Patients and participants: Twenty adult patients affected by severe sep- sis or septic shock with plasma values of PC \ 50%. Interven- tions: Patients were treated with PC concentrate (Ceprotin 2\u2013\u2013Baxter) with a starting bolus followed by a continuous infusion for 72 h [3 IU/ (kg h)]. Measurements and results: PC activity, WBC, platelets, D-Dimer, fibrinogen, PT, aPTT, AT III, lactate, Sepsis-related Organ Failure Assess- ment (SOFA), Disseminated Intravascular Coagulation (DIC) score, adverse events, and mortality were measured. Baseline plasma PC activity was 34.5 \ub1 9.1%. PC con- centrate normalized the PC activity in all patients within 48 h, and then remained stable for the following days. At baseline, several patients showed abnormal PT, aPTT, platelets values, and lactate levels. During the study period, there was a significant increase of platelets, fibrinogen, PT, AT III, and a significant decrease of D-Dimer, aPTT, DIC score, and lac- tate. No adverse reactions (hemorrhage or thrombosis) were observed. Mortality at 28 days was 35%. Conclusions: Our pilot study shows that the administration of PC concentrate to patients having con- traindications to the treatment with activated PC was safe and possibly useful to control the coagulopathy triggered and sustained by sepsis. A randomized, double blind study in patients with severe sepsis and con- traindications to activated PC administration would be advisable to state the safety and the possible role of this product in the treatment of severe sepsis