Computer Simulation (Latest Articles)

Latest indexed articles for 'Computer Simulation'

Articles 1 to 10 of 200:

Analysis of factors associated with volumetric data errors in gamma knife radiosurgery.

25 Nov 2009 OBJECT: Gamma knife (GK) surgery is an important part of the treatment armamentarium for benign and malignant brain tumors. In general, quantitative volumetrical analysis of the tumor on neuroimaging studies is the most reliable method of assessment ...
rec_pub_19039257-analysis-factors-associated-volumetric-data-errors-gamma-knife.htm

Mutual exchange of kinetic properties by extended mutagenesis in two short LOV domain proteins from Pseudomonas putida.

Nov 2009 We previously characterized a LOV protein PpSB2-LOV, present in the common soil bacterium Pseudomonas putida, that exhibits a plant phototropin LOV-like photochemistry [Krauss, U., Losi, A., Gartner, W., Jaeger, K. E., and Eggert, T. (2005) Phys. ...
rec_pub_19772355-mutual-exchange-kinetic-properties-extended-mutagenesis-two-short-lov.htm

Predicting structurally conserved contacts for homologous proteins using sequence conservation filters.

30 Oct 2009 The prediction of intramolecular contacts has a useful application in predicting the three-dimensional structures of proteins. The accuracy of the template-based contact prediction methods depends on the quality of the template structures. To reduce ...
rec_pub_19475704-predicting-structurally-conserved-contacts-homologous-proteins-using.htm

Application of the fuzzy-oil-drop model to membrane protein simulation.

30 Oct 2009 The analysis of structural properties and biological activity of membrane proteins requires long lasting simulation of molecular dynamics. The large number of atoms present in protein molecule, membrane (phospholipids), and water environment makes ...
rec_pub_19455711-application-fuzzy-oil-drop-model-membrane-protein-simulation.htm

Targeted molecular dynamics reveals overall common conformational changes upon hybrid domain swing-out in beta3 integrins.

30 Oct 2009 The beta3 integrin family members alphaIIbeta3 and alphaVbeta3 signal bidirectionally through long-range allosteric changes, including a transition from a bent unliganded-closed low-affinity state to an extended liganded-open high-affinity state. To ...
rec_pub_19455709-targeted-molecular-dynamics-reveals-overall-common-conformational.htm

Native state dynamics and mechanical properties of human topoisomerase I within a structure-based coarse-grained model.

30 Oct 2009 A coarse grained molecular dynamics model with an implicit solvent is used to elucidate properties of the human topoisomerase I. The model is defined through the native structure and it allows covering significantly longer time scales than in all ...
rec_pub_19452556-native-state-dynamics-mechanical-properties-human-topoisomerase.htm

A distance-dependent atomic knowledge-based potential and force for discrimination of native structures from decoys.

30 Oct 2009 The purpose of this article is to introduce a novel model for discriminating correctly folded proteins from well designed decoy structures using mechanical interatomic forces. In our model, we consider a protein as a collection of springs and the ...
rec_pub_19452553-a-distance-dependent-atomic-knowledge-based-potential-force.htm

Template-free protein structure prediction and quality assessment with an all-atom free-energy model.

30 Oct 2009 Biophysical forcefields have contributed less than originally anticipated to recent progress in protein structure prediction. Here, we have investigated the selectivity of a recently developed all-atom free-energy forcefield for protein structure ...
rec_pub_19422063-template-free-protein-structure-prediction-quality-assessment-atom.htm

Substrate binding modifies the hinge bending characteristics of human 3-phosphoglycerate kinase: a molecular dynamics study.

30 Oct 2009 3-Phosphogycerate kinase (PGK) is a two domain enzyme, with a binding site of the 1,3-bisphosphoglycerate on the N-domain and of the ADP on the C-domain. To transfer a phosphate group the enzyme has to undergo a hinge bending motion from open to ...
rec_pub_19422062-substrate-binding-modifies-hinge-bending-characteristics-human-3.htm

Alternative applications of guided surgery: precise outlining of the lateral window in antral sinus bone grafting.

30 Oct 2009 Computed tomography (CT) and the application of CT-based guided implant surgery allow clinicians to provide enhanced precision and accuracy in implant surgery. Because of the difficulty in transferring a patient's often complex anatomic sinus ...
rec_pub_19835747-alternative-applications-guided-surgery-precise-outlining-lateral.htm

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