scholarly journals Shift-field refinement of macromolecular atomic models

2020 ◽  
Vol 76 (12) ◽  
pp. 1192-1200
Author(s):  
K. Cowtan ◽  
S. Metcalfe ◽  
P. Bond
Keyword(s):  
Diffraction Pattern ◽  
Crystallographic Structure ◽  
Model Parameters ◽  
Molecular Replacement ◽  
Macromolecular Crystallography ◽  
Initial Model ◽  
New Approach ◽  
Structure Solution ◽  
Uncertainty Parameters ◽  
Key Parameter

The aim of crystallographic structure solution is typically to determine an atomic model which accurately accounts for an observed diffraction pattern. A key step in this process is the refinement of the parameters of an initial model, which is most often determined by molecular replacement using another structure which is broadly similar to the structure of interest. In macromolecular crystallography, the resolution of the data is typically insufficient to determine the positional and uncertainty parameters for each individual atom, and so stereochemical information is used to supplement the observational data. Here, a new approach to refinement is evaluated in which a `shift field' is determined which describes changes to model parameters affecting whole regions of the model rather than individual atoms only, with the size of the affected region being a key parameter of the calculation which can be changed in accordance with the resolution of the data. It is demonstrated that this approach can improve the radius of convergence of the refinement calculation while also dramatically reducing the calculation time.

scholarly journals REdiii: a pipeline for automated structure solution

2015 ◽  
Vol 71 (5) ◽  
pp. 1059-1067 ◽  
Author(s):  
Markus-Frederik Bohn ◽  
Celia A. Schiffer
Keyword(s):  
High Throughput ◽  
Scientific Discovery ◽  
Workflow Engine ◽  
Quality Data ◽  
Crystallographic Structure ◽  
Molecular Replacement ◽  
High Quality Data ◽  
Adaptive Workflow ◽  
Structure Solution ◽  
Integrated Software

High-throughput crystallographic approaches require integrated software solutions to minimize the need for manual effort.REdiiiis a system that allows fully automated crystallographic structure solution by integrating existing crystallographic software into an adaptive and partly autonomous workflow engine. The program can be initiated after collecting the first frame of diffraction data and is able to perform processing, molecular-replacement phasing, chain tracing, ligand fitting and refinement without further user intervention. Preset values for each software component allow efficient progress with high-quality data and known parameters. The adaptive workflow engine can determine whether some parameters require modifications and choose alternative software strategies in case the preconfigured solution is inadequate. This integrated pipeline is targeted at providing a comprehensive and efficient approach to screening for ligand-bound co-crystal structures while minimizing repetitiveness and allowing a high-throughput scientific discovery process.

scholarly journals Approaches toab initiomolecular replacement of α-helical transmembrane proteins

2017 ◽  
Vol 73 (12) ◽  
pp. 985-996 ◽  
Author(s):  
Jens M. H. Thomas ◽  
Felix Simkovic ◽  
Ronan Keegan ◽  
Olga Mayans ◽  
Chengxin Zhang ◽  
...  
Keyword(s):  
Ab Initio ◽  
Transmembrane Protein ◽  
Protein Structures ◽  
Transmembrane Proteins ◽  
Crystallographic Structure ◽  
Molecular Replacement ◽  
Search Models ◽  
Contact Information ◽  
Structure Solution ◽  
The Ideal

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of theAMPLEmolecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived fromab initiomodels generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, butab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

scholarly journals A New Approach to Group Multi-Objective Optimization under Imperfect Information and Its Application to Project Portfolio Optimization

2021 ◽  
Vol 11 (10) ◽  
pp. 4575
Author(s):  
Eduardo Fernández ◽  
Nelson Rangel-Valdez ◽  
Laura Cruz-Reyes ◽  
Claudia Gomez-Santillan
Keyword(s):  
Portfolio Optimization ◽  
Imperfect Information ◽  
Model Parameters ◽  
Final Decision ◽  
Project Portfolio ◽  
Objective Functions ◽  
Multi Objective Optimization ◽  
New Approach ◽  
Multi Objective ◽  
Group Member

This paper addresses group multi-objective optimization under a new perspective. For each point in the feasible decision set, satisfaction or dissatisfaction from each group member is determined by a multi-criteria ordinal classification approach, based on comparing solutions with a limiting boundary between classes “unsatisfactory” and “satisfactory”. The whole group satisfaction can be maximized, finding solutions as close as possible to the ideal consensus. The group moderator is in charge of making the final decision, finding the best compromise between the collective satisfaction and dissatisfaction. Imperfect information on values of objective functions, required and available resources, and decision model parameters are handled by using interval numbers. Two different kinds of multi-criteria decision models are considered: (i) an interval outranking approach and (ii) an interval weighted-sum value function. The proposal is more general than other approaches to group multi-objective optimization since (a) some (even all) objective values may be not the same for different DMs; (b) each group member may consider their own set of objective functions and constraints; (c) objective values may be imprecise or uncertain; (d) imperfect information on resources availability and requirements may be handled; (e) each group member may have their own perception about the availability of resources and the requirement of resources per activity. An important application of the new approach is collective multi-objective project portfolio optimization. This is illustrated by solving a real size group many-objective project portfolio optimization problem using evolutionary computation tools.

scholarly journals Twodimensional Axialsymmetrical Hydrodynamical Simulations of PN-Evolution

1993 ◽  
Vol 155 ◽  
pp. 373-373
Author(s):  
J. Zweigle ◽  
M. Bremer ◽  
M. Grewing
Keyword(s):  
Numerical Method ◽  
Central Star ◽  
Density Contrast ◽  
Initial Model ◽  
Cylindrical Coordinates ◽  
Model Parameter ◽  
Thick Disks ◽  
Red Giant ◽  
Hydrodynamical Simulations ◽  
Key Parameter

In order to investigate the early evolution of planetary nebulae (PNe) we solved numerically the hydrodynamical equations in cylindrical coordinates (r, z) assuming azimutal symmetry. The numerical method used is described in detail by Mair et al. (1988). Our simulations model the interaction of a fast, tenuous, spherical symmetrical central star wind with a slow, dense, aspherical Red Giant Envelope (RGE) expelled from the progenitor star. For the aspherical RGE with a polar/equatorial density contrast we used the initial model given by Mellema et al. (1991) in cylindrical coordinates. We have investigated the influence of each initial model parameter upon the evolution of PNe. Thereby we confirm that the polar/equatorial density contrast in the RGE and the thickness of the RGE-disk play an important role for the morphology of PNe. In agreement with the results from Mellema et al. (1991). The polar/equatorial density contrast in the RGE influences the ratio of the distances of the bright inner rim to the central star in z- and r-direction. This ratio increases with decreasing polar/equatorial density contrast. We find the thickness of the RGE-disk to be a key parameter for getting an elliptical or a butterfly PN: thin RGE-disks produce the first type of nebulae, thick disks the latter. We thank G. Mair, E. Müller and W. Hillebrandt for making available to us a copy of the SADIE code.

scholarly journals Novel methods of estimating relative pollen productivity: A key parameter for reconstruction of past land cover from pollen records

2019 ◽  
Vol 43 (6) ◽  
pp. 731-753 ◽  
Author(s):  
Yiman Fang ◽  
Chunmei Ma ◽  
M Jane Bunting
Keyword(s):  
Land Cover ◽  
Empirical Data ◽  
Alternative Methods ◽  
Model Parameters ◽  
Value Analysis ◽  
Pollen Productivity ◽  
Tropical China ◽  
The Relationship ◽  
Pollen Records ◽  
Key Parameter

Reconstructing land cover from pollen data using mathematical models of the relationship between them has the potential to translate the many thousand pollen records produced over the last 100 years (over 2300 radiocarbon-dated pollen records exist for the UK alone) into formats relevant to ecologists, archaeologists and climate scientists. However, the reliability of these reconstructions depends on model parameters. A key parameter is Relative Pollen Productivity (RPP), usually estimated from empirical data using ‘Extended R Value analysis’ (ERV analysis). Lack of RPP estimates for many regions is currently a major limitation on reconstructing global land cover. We present two alternatives to ERV analysis, the Modified Davis Method and an iteration method, which use the same underlying model of the relationship between pollen and vegetation to estimate RPP from empirical data, but with different assumptions. We test them in simulation against ERV analysis, and use a case study of a problematic empirical dataset to determine whether they have the potential to increase the speed and geographic range of RPP estimation. The two alternative methods are shown to perform at least as well as ERV analysis in simulation. We also present new RPP estimates from southeastern sub-tropical China for nine taxa estimated using the Modified Davis Method. Adding these two methods to the ‘toolkit’ for land cover reconstruction from pollen records opens up the possibility to estimate a key parameter from existing datasets with less field time than using current methods. This can both speed up the inclusion of more of the globe in past land cover mapping exercises such as the PAGES Landcover6k working group and improve our understanding of how this parameter varies within a single taxon and the factors control that variation.

scholarly journals A New Extended-F Family: Properties and Applications to Lifetime Data

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Saima K. Khosa ◽  
Ahmed Z. Afify ◽  
Zubair Ahmad ◽  
Mi Zichuan ◽  
Saddam Hussain ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Maximum Likelihood Estimators ◽  
Real Data ◽  
Model Parameters ◽  
Additional Parameter ◽  
Alpha Power ◽  
New Approach ◽  
New Class ◽  
Mathematical Properties ◽  
Extended Weibull Distribution

In this article, a new approach is used to introduce an additional parameter to a continuous class of distributions. The new class is referred to as a new extended-F family of distributions. The new extended-Weibull distribution, as a special submodel of this family, is discussed. General expressions for some mathematical properties of the proposed family are derived, and maximum likelihood estimators of the model parameters are obtained. Furthermore, a simulation study is provided to evaluate the validity of the maximum likelihood estimators. Finally, the flexibility of the proposed method is illustrated via two applications to real data, and the comparison is made with the Weibull and some of its well-known extensions such as Marshall–Olkin Weibull, alpha power-transformed Weibull, and Kumaraswamy Weibull distributions.

scholarly journals The structure of rice weevil pectin methylesterase

2014 ◽  
Vol 70 (11) ◽  
pp. 1480-1484 ◽  
Author(s):  
David C. Teller ◽  
Craig A. Behnke ◽  
Kirk Pappan ◽  
Zicheng Shen ◽  
John C. Reese ◽  
...  
Keyword(s):  
Reaction Mechanisms ◽  
Cell Walls ◽  
Sitophilus Oryzae ◽  
Pectin Methylesterase ◽  
Crystal Form ◽  
Erwinia Chrysanthemi ◽  
Rice Weevil ◽  
Molecular Replacement ◽  
Structural Comparison ◽  
Structure Solution

Rice weevils (Sitophilus oryzae) use a pectin methylesterase (EC 3.1.1.11), along with other enzymes, to digest cell walls in cereal grains. The enzyme is a right-handed β-helix protein, but is circularly permuted relative to plant and bacterial pectin methylesterases, as shown by the crystal structure determination reported here. This is the first structure of an animal pectin methylesterase. Diffraction data were collected to 1.8 Å resolution some time ago for this crystal form, but structure solution required the use of molecular-replacement techniques that have been developed and similar structures that have been deposited in the last 15 years. Comparison of the structure of the rice weevil pectin methylesterase with that fromDickeya dandantii(formerlyErwinia chrysanthemi) indicates that the reaction mechanisms are the same for the insect, plant and bacterial pectin methylesterases. The similarity of the structure of the rice weevil enzyme to theEscherichia colilipoprotein YbhC suggests that the evolutionary origin of the rice weevil enzyme was a bacterial lipoprotein, the gene for which was transferred to a primitive ancestor of modern weevils and other Curculionidae. Structural comparison of the rice weevil pectin methylesterase with plant and bacterial enzymes demonstrates that the rice weevil protein is circularly permuted relative to the plant and bacterial molecules.

Study on Corner Contact Shock of Gear Transmission by ADAMS Software

2015 ◽  
Vol 778 ◽  
pp. 205-211
Author(s):  
Li He ◽  
Jin Yuan Tang
Keyword(s):  
Penetration Depth ◽  
Impact Velocity ◽  
Impact Force ◽  
Ansys Software ◽  
New Approach ◽  
Adams Software ◽  
Simulation Results ◽  
The Impact ◽  
The Relationship ◽  
Key Parameter

Solving gear meshing impact force problems by using ADAMS software is studied.A pair of tooth meshing model is established based on UG, modal neutral file is generated by using ANSYS software, calculating gear meshing impact after Importing ADAMS. The relationship between the impact velocity and the impact force by taking reasonable key parameter about penetration depth in ADAMS simulation.A new approach for studying gear meshing impact is proposed here, and the simulation results show that ADAMS software is a very useful tool for solving gear corner contact shock problems outside the normal path of action line.

AN APPROACH TO NATURAL STROKE EXTRACTION FOR OFF-LINE LOOSELY-CONSTRAINED HANDWRITTEN CHINESE CHARACTERS

2003 ◽  
Vol 17 (08) ◽  
pp. 1483-1513
Author(s):  
DANIEL S. YEUNG ◽  
H. S. FONG ◽  
ERIC C. C. TSANG ◽  
WENHAO SHU ◽  
XIAOLONG WANG
Keyword(s):  
Performance Tuning ◽  
Model Parameters ◽  
Chinese Characters ◽  
Personal Writing ◽  
New Approach ◽  
Stroke Extraction ◽  
Fuzzy Partitioning ◽  
Stroke Models ◽  
Matching Strategy ◽  
Ranked List

This paper proposes a new approach to extracting natural strokes from the skeletons of loosely-constrained, off-line handwritten Chinese characters. It admits the output substrokes from a previously proposed fuzzy substroke extractor as its inputs. By identifying a number of expected ambiguities which include mutual similarities, unstable touches and joint/cross distortions, fuzzy stroke models are constructed and a "hit-all" fuzzy stroke matching strategy is pursued. Fuzzy partitioning technique is used to generate a ranked list of consistent stroke sets from the set of fuzzy strokes being identified. With this approach, a maximum of 20 distinct natural stroke classes can be extracted from each input character, together with an estimate on the actual count of strokes which compose the character. Our system offers a number of performance tuning capabilities such as the computation of the fuzzy scores of each extracted stroke, the adjustment on the fuzzy stroke model parameters, and the potential of incorporating one's personal writing styles into our methodology.

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