Temat: comparative modeling

Skocz do pozycji: 1.

Tytuł:: Homology modeling of the G protein-coupled receptors
Autorzy:: Mordalski, Stefan
Kościółek, Tomasz
Dostawca treści:: Repozytorium Uniwersytetu Jagiellońskiego

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Skocz do pozycji: 2.

Tytuł:: Protein modeling and structure prediction with a reduced representation.
Autorzy:: Kolinski, Andrzej
Tematy:: Monte Carlo simulations
structure prediction
comparative modeling
lattice proteins
protein folding; Pokaż więcej
Wydawca:: Polskie Towarzystwo Biochemiczne
Powiązania:: https://bibliotekanauki.pl/articles/1043267.pdf Link otwiera się w nowym oknie
Opis:: Protein modeling could be done on various levels of structural details, from simplified lattice or continuous representations, through high resolution reduced models, employing the united atom representation, to all-atom models of the molecular mechanics. Here I describe a new high resolution reduced model, its force field and applications in the structural proteomics. The model uses a lattice representation with 800 possible orientations of the virtual alpha carbon-alpha carbon bonds. The sampling scheme of the conformational space employs the Replica Exchange Monte Carlo method. Knowledge-based potentials of the force field include: generic protein-like conformational biases, statistical potentials for the short-range conformational propensities, a model of the main chain hydrogen bonds and context-dependent statistical potentials describing the side group interactions. The model is more accurate than the previously designed lattice models and in many applications it is complementary and competitive in respect to the all-atom techniques. The test applications include: the ab initio structure prediction, multitemplate comparative modeling and structure prediction based on sparse experimental data. Especially, the new approach to comparative modeling could be a valuable tool of the structural proteomics. It is shown that the new approach goes beyond the range of applicability of the traditional methods of the protein comparative modeling.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 3.

Tytuł:: TRACER. A new approach to comparative modeling that combines threading with free-space conformational sampling
Autorzy:: Trojanowski, Sebastian
Rutkowska, Aleksandra
Kolinski, Andrzej
Tematy:: protein comparative modeling
coarse grained protein models
protein threading
Monte Carlo simulations
replica exchange Monte Carlo; Pokaż więcej
Wydawca:: Polskie Towarzystwo Biochemiczne
Powiązania:: https://bibliotekanauki.pl/articles/1040439.pdf Link otwiera się w nowym oknie
Opis:: A new approach to comparative modeling of proteins, TRACER, is described and benchmarked against classical modeling procedures. The new method unifies true three-dimensional threading with coarse-grained sampling of query protein conformational space. The initial sequence alignment of a query protein with a template is not required, although a template needs to be somehow identified. The template is used as a multi-featured fuzzy three-dimensional scaffold. The conformational search for the query protein is guided by intrinsic force field of the coarse-grained modeling engine CABS and by compatibility with the template scaffold. During Replica Exchange Monte Carlo simulations the model chain representing the query protein finds the best possible structural alignment with the template chain, that also optimizes the intra-protein interactions as approximated by the knowledge based force field of CABS. The benchmark done for a representative set of query/template pairs of various degrees of sequence similarity showed that the new method allows meaningful comparative modeling also for the region of marginal, or non-existing, sequence similarity. Thus, the new approach significantly extends the applicability of comparative modeling.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 4.

Tytuł:: Implementation and evaluation of new protocol for comparative modeling of protein structures
Autorzy:: Strumillo, M.
Dawid, A. E.
Szczasiuk, A.
Gront, D.
Tematy:: protein structure prediction
comparative modeling
protein threading
protein alignment
BioShell
Rosetta
przewidywanie struktury białek
modelowanie porównawcze
gwintowania białka
wyrównanie białka; Pokaż więcej
Wydawca:: Politechnika Gdańska
Powiązania:: https://bibliotekanauki.pl/articles/1935813.pdf Link otwiera się w nowym oknie
Opis:: Template-based modeling (termed also Comparative or Homology Modeling) of a protein structure is one of ubiquitous tasks of structural bioinfor matics. The method can deliver model structures important for testing biological hypotheses, virtual docking and drug design. The performance of these methods is evaluated every two years during a Critical Assessment of Protein Structure Prediction (CASP) experiment. In this contribution we present a new automated protocol for template-base d modeling, which combines computational tools recently developed in our laboratory: the dat abase of protein domain structures (BDDB) with one dimensional and three dimensional thread ing applications. The protocol was tested during a CASP11 experiment.
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 5.

Tytuł:: Correction of the parametric model of the Day-Ahead Market system using the Artificial Neural Network
Autorzy:: Marlęga, Radosław
Tematy:: artificial neural network
day-ahead market
modeling
simulation
comparative research
model sensitivity testing; Pokaż więcej
Wydawca:: Uniwersytet Przyrodniczo-Humanistyczny w Siedlcach
Powiązania:: https://bibliotekanauki.pl/articles/2175158.pdf Link otwiera się w nowym oknie
Opis:: The paper shows that it is possible to correct the identification model of the Day-Ahead Market system by employing the Perceptron Artificial Neural Network. First, a simulation model of the DAM system at the POLPX has been built, and then it has been shown how the model can be corrected so that the weighted average electricity prices obtained are close enough to the exchange-quoted ones. Next, simulation, comparative and sensitivity studies of the model were carried out for forecast data for four characteristic hours: 6, 12, 18, and 24 of the following year. Many interesting research results were obtained, including a result of sensitivity testing it was shown that the obtained models can be used in forecasting studies.
Dostawca treści:: Biblioteka Nauki

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