Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Conference Object Citation - WoS: 3Citation - Scopus: 3Template Scoring Methods for Protein Torsion Angle Prediction(Springer-Verlag Berlin, 2015) Aydin, Zafer; Baker, David; Noble, William StaffordPrediction of backbone torsion angles provides important constraints about the 3D structure of a protein and is receiving a growing interest in the structure prediction community. In this paper, we introduce a three-stage machine learning classifier to predict the 7-state torsion angles of a protein. The first two stages employ dynamic Bayesian and neural networks to produce an ab-initio prediction of torsion angle states starting from sequence profiles. The third stage is a committee classifier, which combines the ab-initio prediction with a structural frequency profile derived from templates obtained by HHsearch. We develop several structural profile models and obtain significant improvements over the Laplacian scoring technique through: (1) scaling templates by integer powers of sequence identity score, (2) incorporating other alignment scores as multiplicative factors (3) adjusting or optimizing parameters of the profile models with respect to the similarity interval of the target. We also demonstrate that the torsion angle prediction accuracy improves at all levels of target-template similarity even when templates are distant from the target. The improvement is at significantly higher rates as template structures gradually get closer to target.Article Citation - WoS: 2Citation - Scopus: 2Structural Profile Matrices for Predicting Structural Properties of Proteins(World Scientific Publ Co Pte Ltd, 2020-07-10) Azginoglu, Nuh; Aydin, Zafer; Celik, MetePredicting structural properties of proteins plays a key role in predicting the 3D structure of proteins. In this study, new structural profile matrices (SPM) are developed for protein secondary structure, solvent accessibility and torsion angle class predictions, which could be used as input to 3D prediction algorithms. The structural templates employed in computing SPMs are detected by eight alignment methods in LOMETS server, gap affine alignment method, ScanProsite, PfamScan, and HHblits. The contribution of each template is weighted by its similarity to target, which is assessed by several sequence alignment scores. For comparison, the SPMs are also computed using Homolpro, which uses BLAST for target template alignments and does not assign weights to templates. Incorporating the SPMs into DSPRED classifier, the prediction accuracy improves significantly as demonstrated by cross-validation experiments on two difficult benchmarks. The most accurate predictions are obtained using the SPMs derived by threading methods in LOMETS server. On the other hand, the computational cost of computing these SPMs was the highest.Book Part Citation - Scopus: 3ROSE: A Novel Approach for Protein Secondary Structure Prediction(Springer Science and Business Media Deutschland GmbH, 2021) Görmez, Yasin; Aydin, ZaferThree-dimensional structure of protein gives important information about protein’s function. Since it is time-consuming and costly to find the structure of protein by experimental methods, estimation of three-dimensional structures of proteins through computational methods has been an efficient alternative. One of the most important steps for the 3-D protein structure prediction is protein secondary structure prediction. Proteins which contain different number and sequences of amino acids may have similar structures. Thus, extracting appropriate input features has crucial importance for secondary structure prediction. In this study, a novel model, ROSE, is proposed for secondary structure prediction that obtains probability distributions as a feature vector by using two position specific scoring matrices obtained by PSIBLAST and HHblits. ROSE is a two-stage hybrid classifier that uses a one-dimensional bi-directional recurrent neural network at the first stage and a support vector machine at the second stage. It is also combined with DSPRED method, which employs dynamic Bayesian networks and a support vector machine. ROSE obtained comparable results to DSPRED in cross-validation experiments performed on a difficult benchmark and can be used as an alternative to protein secondary structure prediction. © 2021 Elsevier B.V., All rights reserved.Article Citation - WoS: 6Citation - Scopus: 8Dimensionality Reduction for Protein Secondary Structure and Solvent Accesibility Prediction(World Scientific Publ Co Pte Ltd, 2018-10) Aydin, Zafer; Kaynar, Oguz; Gormez, YasinSecondary structure and solvent accessibility prediction provide valuable information for estimating the three dimensional structure of a protein. As new feature extraction methods are developed the dimensionality of the input feature space increases steadily. Reducing the number of dimensions provides several advantages such as faster model training, faster prediction and noise elimination. In this work, several dimensionality reduction techniques have been employed including various feature selection methods, autoencoders and PCA for protein secondary structure and solvent accessibility prediction. The reduced feature set is used to train a support vector machine at the second stage of a hybrid classifier. Cross-validation experiments on two difficult benchmarks demonstrate that the dimension of the input space can be reduced substantially while maintaining the prediction accuracy. This will enable the incorporation of additional informative features derived for predicting the structural properties of proteins without reducing the accuracy due to overfitting.Article A Comparative Study of Unet Variants for Low-Grade Glioma Segmentation in Magnetic Resonance Imaging(Inonu University, 2025-06-25) Guzel, Yasin; Aydin, ZaferBrain tumors originating from glial cells are pathological entities that significantly impact quality of life and are classified based on their malignancy into low-grade gliomas (LGGs) and high-grade gliomas (HGGs). While the more aggressive HGGs have been extensively studied, LGGs are of critical importance for early diagnosis due to their potential progression to HGGs if left untreated. This has driven researchers to develop methods for the rapid and consistent diagnosis of LGGs. In this study, three models—UNet, Transformer UNet, and Super Vision UNet—were comparatively evaluated for the automatic segmentation of LGGs using magnetic resonance imaging (MRI) data. Multimodal MRI scans from 110 patients, retrieved from The Cancer Imaging Archive (TCIA), were used to train the models. Performance was evaluated using Dice Coefficient, Tversky Index, and Intersection over Union (IoU) metrics. The Super Vision UNet achieves the highest Dice (0.9115) and Tversky (0.9154) scores, while the Transformer UNet attains the highest IoU (0.8789). Both advanced models demonstrate superior segmentation performance with lower loss values compared to the conventional UNet. Visual outputs indicate that the modern architectures delineate tumor contours with greater precision. These results highlight the effectiveness and reliability of contemporary UNet-based and Transformer-based architectures in segmenting complex tumor structures such as LGGs. Integrating these models into clinical decision support systems holds promise for enhancing the speed and accuracy of the diagnostic process. © 2025 Elsevier B.V., All rights reserved.