scholarly journals TRACER. A new approach to comparative modeling that combines threading with free-space conformational sampling.

2010 ◽  
Vol 57 (1) ◽  
Author(s):  
Sebastian Trojanowski ◽  
Aleksandra Rutkowska ◽  
Andrzej Kolinski
Keyword(s):  
Force Field ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Comparative Modeling ◽  
Query Protein ◽  
New Method ◽  
Conformational Space ◽  
Coarse Grained ◽  
Conformational Search ◽  
New Approach

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.

scholarly journals Protein modeling and structure prediction with a reduced representation.

2004 ◽  
Vol 51 (2) ◽  
pp. 349-371 ◽  
Author(s):  
Andrzej Kolinski
Keyword(s):  
High Resolution ◽  
Force Field ◽  
Structure Prediction ◽  
Comparative Modeling ◽  
Protein Modeling ◽  
Conformational Space ◽  
Structural Proteomics ◽  
New Approach ◽  
Statistical Potentials ◽  
Alpha Carbon

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.

IN SEARCH OF THE PROTEIN NATIVE STATE WITH A PROBABILISTIC SAMPLING APPROACH

2011 ◽  
Vol 09 (03) ◽  
pp. 383-398 ◽  
Author(s):  
BRIAN OLSON ◽  
KEVIN MOLLOY ◽  
AMARDA SHEHU
Keyword(s):  
Structure Prediction ◽  
Computational Models ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Search Space ◽  
Conformational Space ◽  
Conformational Search ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Native State

The three-dimensional structure of a protein is a key determinant of its biological function. Given the cost and time required to acquire this structure through experimental means, computational models are necessary to complement wet-lab efforts. Many computational techniques exist for navigating the high-dimensional protein conformational search space, which is explored for low-energy conformations that comprise a protein's native states. This work proposes two strategies to enhance the sampling of conformations near the native state. An enhanced fragment library with greater structural diversity is used to expand the search space in the context of fragment-based assembly. To manage the increased complexity of the search space, only a representative subset of the sampled conformations is retained to further guide the search towards the native state. Our results make the case that these two strategies greatly enhance the sampling of the conformational space near the native state. A detailed comparative analysis shows that our approach performs as well as state-of-the-art ab initio structure prediction protocols.

scholarly journals Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
P. M. Pieczywek ◽  
W. Płaziński ◽  
A. Zdunek
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Large Scale ◽  
Dissipative Particle Dynamics ◽  
Three Dimensional ◽  
Structural Features ◽  
Particle Dynamics ◽  
Distribution Functions ◽  
Coarse Grained ◽  
Dynamics Model

Abstract In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. The model of the homogalacturonan was designed to test the ability of the formation of large-scale structures via hydrogen bonding in water. The extraction of coarse-grained parameters from atomistic molecular dynamics was achieved by means of the proposed molecule aggregation algorithm based on an iterative nearest neighbour search. A novel approach to a time-scale calibration scheme based on matching the average velocities of coarse-grained particles enabled the DPD forcefield to reproduce essential structural features of homogalacturonan molecular chains. The successful application of the proposed parametrization method allowed for the reproduction of the shapes of radial distribution functions, particle velocities and diffusivity of the atomistic molecular dynamics model using DPD force field. The structure of polygalacturonic acid molecules was mapped into the DPD force field by means of the distance and angular bond characteristics, which closely matched the MD results. The resulting DPD trajectories showed that randomly dispersed homogalacturonan chains had a tendency to aggregate into highly organized 3D structures. The final structure resembled a three-dimensional network created by tightly associated homogalacturonan chains organized into thick fibres.

The Simulation of Apparent Directional Emissivity in a Three-Dimensional Non-Isothermal Medium by the DRESOR Method

2011 ◽  
Author(s):  
Qiang Cheng ◽  
Xiang-Yu Zhang ◽  
Zhi-Chao Wang ◽  
Huai-Chun Zhou ◽  
Lv-Bin Wu
Keyword(s):  
Absorption Coefficient ◽  
Glass Melting ◽  
Three Dimensional ◽  
Heating Furnace ◽  
New Method ◽  
Scattering Coefficient ◽  
New Approach ◽  
Isothermal Medium ◽  
Directional Emissivity ◽  
Industrial Heating

The emissivity as a thermal property plays an important role required for heat transfer calculations and temperature measurement. In an isothermal purely absorption medium, the emissivity can be calculated by the formula, but no general formula for the emissivity will suit the system with scattering of medium and reflection of walls in a coal-fired boiler or an industrial heating furnace. In this study, a new approach was proposed to scale the apparent field directional emissivity by DRESOR method combined with two-color method in a three-dimensional non-isothermal participating medium with reflection of walls. The results obtained by the new method were compared with those calculated by the formula to verify the validity and accuracy of new method in an isothermal purely absorption medium. Then the new method was extended to examine the effect of absorption coefficient, scattering coefficient and reflection of walls on the apparent directional emissivity in the isothermal and non-isothermal cases. It is found that when there is scattering in the medium, the emissivity cannot be equal to the entity, even if the medium is optically thick. In the condition of walls with cold or low temperature, such as in the case of a coal-fired boiler, the apparent emissivity increases with the increase of absorption coefficient and reflectivity of walls, because radiation from hot media plays a dominated role in emissivity in this situation; Meanwhile, in the case of walls with high temperature, such as in the case of an industrial heating furnace in metallurgy or glass melting industry, the apparent emissivity decreases with the increase of absorption coefficient, because the emissivity is mainly determined by the wall radiation in this situation. And when scattering coefficient increases, the apparent emissivity decreases for all isothermal and non-isothermal cases.

scholarly journals A new method for detecting solar atmospheric gravity waves

2020 ◽  
Vol 379 (2190) ◽  
pp. 20200178 ◽  
Author(s):  
Daniele Calchetti ◽  
Stuart M. Jefferies ◽  
Bernhard Fleck ◽  
Francesco Berrilli ◽  
Dmitriy V. Shcherbik
Keyword(s):  
Solar Atmosphere ◽  
Gravity Waves ◽  
Three Dimensional ◽  
Internal Gravity Waves ◽  
New Method ◽  
Ample Evidence ◽  
New Approach ◽  
Wave Dynamics ◽  
Atmospheric Gravity ◽  
Lower Solar Atmosphere

Internal gravity waves have been observed in the Earth’s atmosphere and oceans, on Mars and Jupiter, and in the Sun’s atmosphere. Despite ample evidence for the existence of propagating gravity waves in the Sun’s atmosphere, we still do not have a full understanding of their characteristics and overall role for the dynamics and energetics of the solar atmosphere. Here, we present a new approach to study the propagation of gravity waves in the solar atmosphere. It is based on calculating the three-dimensional cross-correlation function between the vertical velocities measured at different heights. We apply this new method to a time series of co-spatial and co-temporal Doppler images obtained by SOHO/MDI and Hinode/SOT as well as to simulations of upward propagating gravity wave-packets. We show some preliminary results and outline future developments. This article is part of the Theo Murphy meeting issue ‘High-resolution wave dynamics in the lower solar atmosphere’.

A New Approach for the Analysis of Mixture Toxicity Data

1992 ◽  
Vol 26 (9-11) ◽  
pp. 2345-2348 ◽  
Author(s):  
C. N. Haas
Keyword(s):  
Quantitative Analysis ◽  
Mixture Toxicity ◽  
New Method ◽  
Metal Exposure ◽  
Positive Interactions ◽  
Toxicity Data ◽  
Data Set ◽  
New Approach ◽  
Negative Interactions

A new method for the quantitative analysis of multiple toxicity data is described and illustrated using a data set on metal exposure to copepods. Positive interactions are observed for Ni-Pb and Pb-Cr, with weak negative interactions observed for Ni-Cr.

scholarly journals A New Method to Evaluate Trueness and Precision of Digital and Conventional Impression Techniques for Complete Dental Arch

2021 ◽  
Vol 11 (10) ◽  
pp. 4612
Author(s):  
KweonSoo Seo ◽  
Sunjai Kim
Keyword(s):  
Intraclass Correlation ◽  
Three Dimensional ◽  
New Method ◽  
Digital Impression ◽  
Dental Arch ◽  
Digital Models ◽  
Digital Impressions ◽  
Measuring Machine ◽  
Master Model ◽  
Conventional Impression

Purpose: The aim of this study was to present a new method to analyze the three-dimensional accuracy of complete-arch dental impressions and verify the reliability of the method. Additionally, the accuracies of conventional and intraoral digital impressions were compared using the new method. Methods: A master model was fabricated using 14 milled polyetheretherketone cylinders and a maxillary acrylic model. Each cylinder was positioned and named according to its corresponding tooth position. Twenty-five definitive stone casts were fabricated using conventional impressions of the master model. An intraoral scanner was used to scan the master model 25 times to fabricate 25 digital models. A coordinate measuring machine was used to physically probe each cylinder in the master model and definitive casts. An inspection software was used to probe cylinders of digital models. A three-dimensional part coordinate system was defined and used to compute the centroid coordinate of each cylinder. Intraclass correlation coefficient (ICC) was evaluated to examine the reliability of the new method. Independent two sample t-test was performed to compare the trueness and precision of conventional and intraoral digital impressions (α = 0.05). Results: ICC results showed that, the new method had almost perfect reliability for the measurements of the master model, conventional and digital impression. Conventional impression showed more accurate absolute trueness and precision than intraoral digital impression for most of the tooth positions (p < 0.05). Conclusions: The new method was reliable to analyze the three-dimensional deviation of complete-arch impressions. Conventional impression was still more accurate than digital intraoral impression for complete arches.

scholarly journals New Method for Generating New Families of Distributions

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 726
Author(s):  
Lamya A. Baharith ◽  
Wedad H. Aljuhani
Keyword(s):  
Exponential Distribution ◽  
Real Data ◽  
Rate Function ◽  
New Method ◽  
Likelihood Method ◽  
Alpha Power ◽  
Unknown Parameters ◽  
Failure Rate Function ◽  
New Approach ◽  
Numerical Studies

This article presents a new method for generating distributions. This method combines two techniques—the transformed—transformer and alpha power transformation approaches—allowing for tremendous flexibility in the resulting distributions. The new approach is applied to introduce the alpha power Weibull—exponential distribution. The density of this distribution can take asymmetric and near-symmetric shapes. Various asymmetric shapes, such as decreasing, increasing, L-shaped, near-symmetrical, and right-skewed shapes, are observed for the related failure rate function, making it more tractable for many modeling applications. Some significant mathematical features of the suggested distribution are determined. Estimates of the unknown parameters of the proposed distribution are obtained using the maximum likelihood method. Furthermore, some numerical studies were carried out, in order to evaluate the estimation performance. Three practical datasets are considered to analyze the usefulness and flexibility of the introduced distribution. The proposed alpha power Weibull–exponential distribution can outperform other well-known distributions, showing its great adaptability in the context of real data analysis.

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