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A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction.

ABSTRACT: Rhodopsins are seven ?-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling. However, the majority of this progress was made for soluble proteins and further investigations are needed to achieve similar progress for membrane proteins. In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures. Three widely used methodologies were considered: two general methodologies that are commonly applied to soluble proteins and a methodology that uses constraints that are specific for membrane proteins. The test pool consisted of 36 target-template pairs with different sequence similarities that was constructed on the basis of 24 experimental rhodopsin structures taken from the RCSB database. As a result, we showed that all three considered methodologies allow obtaining rhodopsin structures with the quality that is close to the crystallographic one (root mean square deviation (RMSD) of the predicted structure from the corresponding X-ray structure up to 1.5 Å) if the target-template sequence identity is higher than 40%. Moreover, all considered methodologies provided structures of average quality (RMSD < 4.0 Å) if the target-template sequence identity is higher than 20%. Such structures can be subsequently used for further investigation of molecular mechanisms of protein functioning and for the development of modern protein-based biotechnologies.

SUBMITTER: Nikolaev DM

PROVIDER: S-EPMC6068592 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction.

Nikolaev Dmitrii M DM Shtyrov Andrey A AA Panov Maxim S MS Jamal Adeel A Chakchir Oleg B OB Kochemirovsky Vladimir A VA Olivucci Massimo M Ryazantsev Mikhail N MN

ACS omega 20180709 7

Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, signifi ...[more]

PMID: 30087916

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Project description:Motorcycle crash severity is under-researched in Ghana. Thus, the probable risk factors and association between these factors and motorcycle crash severity outcomes is not known. Traditional statistical models have intrinsic assumptions and pre-defined correlations that, if flouted, can generate inaccurate results. In this study, machine learning based algorithms were employed to predict and classify motorcycle crash severity. Machine learning based techniques are non-parametric models without the presumption of relationships between endogenous and exogenous variables. The main aim of this research is to evaluate and compare different approaches to modeling motorcycle crash severity as well as investigating the effect of risk factors on the injury outcomes of motorcycle crashes. Motorcycle crash dataset between 2011 and 2015 was extracted from the National Road Traffic Crash Database at the Building and Road Research Institute (BRRI) in Ghana. The dataset was classified into four injury severity categories: fatal, hospitalized, injured, and damage-only. Three machine learning based models were developed: J48 Decision Tree Classifier, Random Forest (RF) and Instance-Based learning with parameter k (IBk) were employed to model the severity of injury in a motorcycle crash. These machine learning algorithms were validated using 10-fold cross-validation technique. The three machine learning based algorithms were compared with one another and the statistical model: multinomial logit model (MNLM). Also, the relative importance analysis of the attribute was conducted to determine the impact of these attributes on injury severity outcomes. The results of the study reveal that the predictions of machine learning algorithms are superior to the MNLM in accuracy and effectiveness, and the RF-based algorithms show the overall best agreement with the experimental data out of the three machine learning algorithms, for its global optimization and extrapolation ability. Location type, time of the crash, settlement type, collision partner, collision type, road separation, road surface type, the day of the week, and road shoulder condition were found as the critical determinants of motorcycle crash injury severity.

Dataset Information

A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction.

Publications

A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction.

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