55 research outputs found
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
Building Portfolios for the Protein Structure Prediction Problem
International audienceThis paper, concerned with the protein structure prediction problem, aims at automatically selecting the Constraint Satisfaction algorithm best suited to the problem instance at hand. The contribution is twofold. Firstly, the selection criterion is the quality (minimal cost) in expectation of the solution found after a fixed amount of time, as opposed to the expected runtime. Secondly, the presented approach, based on supervised Machine Learning algorithms, considers the original description of the protein structure problem, as opposed to the features related to the SAT or CSP encoding of the problem
A Parallel Framework for Multipoint Spiral Search in ab Initio Protein Structure Prediction
Protein structure prediction is computationally a very challenging problem. A large number of existing search
algorithms attempt to solve the problem by exploring possible structures and finding the one with the minimum free energy. However, these algorithms perform poorly on large sized proteins due to an astronomically wide search space. In this paper, we present a multipoint spiral search framework that uses parallel processing techniques to expedite exploration by starting from different points. In our approach, a set of random initial solutions are generated and distributed to different threads. We allow each thread to run for a predefined period of time. The improved solutions are stored threadwise. When the threads finish, the solutions are merged together and the duplicates are removed. A selected distinct set of solutions are then split to different threads again. In our ab initio protein structure prediction method, we use the three-dimensional face-centred-cubic lattice for structure-backbone mapping. We use both the low resolution hydrophobic-polar energy model and the high-resolution 20Ă—20 energy model for search guiding. The experimental results show that our new parallel framework significantly improves the results obtained by the state-of-the-art single-point search approaches for both energy models on three-dimensional face-centred-cubic lattice. We also experimentally show the effectiveness of mixing energy models within parallel threads
Exact, constraint-based structure prediction in simple protein models
Die Arbeit untersucht die exakte Vorhersage der Struktur von Proteinen in dreidimensionalen, abstrakten Proteinmodellen; insbesondere wird ein exakter Ansatz zur Strukturvorhersage in den HP-Modellen (Lau und Dill, ACS, 1989) des kubischen und kubisch-flächenzentrierten Gitters entwickelt und diskutiert. Im Gegensatz zu heuristischen Methoden liefert das vorgestellte exakte Verfahren beweisbar korrekte Strukturen. HP-Modelle (Hydrophob, Polar) repräsentieren die Rückgratkonformation eines Proteins durch Gitterpunkte und berücksichti\-gen ausschließlich die hydrophobe Wechselwirkung als treibende Kraft bei der Ausbildung der Proteinstruktur. Wesentlich für die erfolgreiche Umsetzung des vorgestellten Verfahrens ist die Verwendung von constraint-basierten Techniken. Im Zentrum steht die Berechnung und Anwendung hydrophober Kerne für die Strukturvorhersage
Biochemical analysis of the W28F mutant of human class Pi glutathione S-transferase
A dissertation submitted in fulfilment of the requirements for the degree of
Master of Science at the University of the Witwatersrand. Johannesburg, October 1996.Glutathione S-transferase (GST) class Pi has two tryptophan residues which are conserved within domain one. Trp38 plays a functional role in sequestering
glutathione at the active site, whereas Trp28 plays a structural role. The effects of the sterically-conservative substitution of Trp28 to Phe were investigated. When the W28F mutant was compared with the wild-type enzyme, mutation of Ttp28 to Phe was not well tolerated and resulted in a dimeric protein with impaired catalytic function and conformational stability. [Abbreviated Abstract. Open document to view full version]AC201
Odyssée au fil des interfaces: de la physico-chimie des macromolécules à l'enveloppe bactérienne, plate-forme interactive du micro-organisme avec son micro-environnement
This find is registered at Portable Antiquities of the Netherlands with number PAN-0001909
The Transmission Electron Microscope
The book "The Transmission Electron Microscope" contains a collection of research articles submitted by engineers and scientists to present an overview of different aspects of TEM from the basic mechanisms and diagnosis to the latest advancements in the field. The book presents descriptions of electron microscopy, models for improved sample sizing and handling, new methods of image projection, and experimental methodologies for nanomaterials studies. The selection of chapters focuses on transmission electron microscopy used in material characterization, with special emphasis on both the theoretical and experimental aspect of modern electron microscopy techniques. I believe that a broad range of readers, such as students, scientists and engineers will benefit from this book
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