FIS-PNN: a hybrid computational method for protein-protein interactions prediction using the secondary structure information (original) (raw)
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FIS-PNN: A hybrid computational method for protein-protein interaction prediction
2011 9th IEEE/ACS International Conference on Computer Systems and Applications (AICCSA), 2011
The study of protein-protein interactions (PPI) is an active area of research in biology because it mediates most of the biological functions in any organism. This work is inspired by the fact that proteins with similar secondary structures mostly share very similar three-dimensional structures, and consequently, very similar functions. As a result, they must interact with each other. In this study we used our approach, namely FIS-PNN, to predict the interacting proteins in yeast from the information of their secondary structures using hybrid machine learning algorithms. Two main stages of our approach are similarity score computation, and classification. The first stage is further divided into three steps: (1) Multiple-sequence alignment, (2) Secondary structure prediction, and (3) Similarity measurement. In the classification stage, several independent first order Sugeno Fuzzy Inference Systems and probabilistic neural networks are generated to model the behavior of similarity scores of all possible proteins pairs. The final results show that the multiple classifiers have significantly improved the performance of the single classifier. Our method, namely FIS-PNN, successfully predicts PPI with 96% of accuracy, a level that is significantly greater than all other sequence-based prediction methods.
Diyete protein eklenmesi sporcuların kardiyovasküler sistemini etkiler mi?
Cukurova Medical Journal
Öz Purpose: Arrhythmias are reproached for most of the sudden cardiac deaths in professional athletes. Also, performance-enhancing dietary supplements have been blamed in recent years. In this study, we aimed to investigate the effect of protein supplements (PS) on regular training athletes. Materials and Methods: 70 male sportsmen (30.0 ± 7.3 year) who regularly train in the gym, were included in the study; 35 used approximately 40 grams of PS daily, while the other half regularly trained without additional PS. All participants underwent ECG, exercise test and results were evaluated by two independent cardiologists. Results: There were no differences between two groups in terms of age, smoking and alcohol use, body mass index, baseline ECG results, effort capacity, heart rate, and blood pressure values. Correlation analyses showed a negative correlation between the age and maximum HR in an effort test. Conclusion: This study showed that using PS in certain does not have any effect on ECG findings, heart rate at both rest and during exercise, effort capacity evaluated by a treadmill test, and blood pressure values of sportsmen. Amaç: Profesyonel sporcularda aritmiler, ani kardiyak ölümlerin çoğundan sorumlu tutulmaktadır. Aynı zamanda, performansı artıran diyet takviyeleri de son yıllarda suçlanmaktadır. Bu çalışmada, protein takviyelerinin (PT) düzenli antreman yapan sporcular üzerindeki etkisini araştırmayı amaçladık. Gereç ve Yöntem: Düzenli olarak antrenman yapan 70 (30.0 ± 7.3 yıl) erkek sporcu çalışmaya dahil edildi; 35 sporcu günde yaklaşık 40 gram PT kullanan, diğer yarısı PT kullanmadan egzersiz yapanlardı. Tüm katılımcılara EKG çekildi, efor testi yapıldı ve sonuçları iki bağımsız kardiyolog tarafından değerlendirildi. Bulgular: İki grup arasında yaş, sigara ve alkol kullanımı, vücut kitle indeksi, başlangıç EKG sonuçları, efor kapasitesi, kalp atım hızı ve kan basıncı değerleri açısından fark yoktu. Korelasyon analizinde, yaş ile efordaki en yüksek kalp hızı arasında negative korelasyon görüldü. Sonuç: Bu çalışma, sporcuların protein tozlarını belirli dozlarda kullandıklarında, kalp atış hızı, hem dinlenme hem egzersiz esnasındaki EKG bulguları, kan basıncı ve egzersiz kapasitesi üzerinde hiç bir etkiye sahip olmadıklarını göstermiştir.
Pemodelan Calponin Ikan Gabus (Channa striata) dengan Phyre2 dan Interaksi dengan Protein Lain
Jurnal Natural Scientiae, 2022
Knowledge of the three-dimensional structure of proteins is very important to understand their character and function at the molecular level. Determination of protein structure in the laboratory is expensive and relatively difficult because it requires sophisticated instruments and takes a long time. As an alternative, an in silico approach can be used to predict the three-dimensional structure of proteins, namely the fold recognition method. The purpose of this study was to create a three-dimensional structure model of snakehead fish (Channa striata) calponin protein using the Phyre2 web server. The target protein sequence was obtained from UniProt KB with code K9LH64. The results of the study showed that the template for building the model was the c1wynA code. The results of the model (MP) evaluation obtained a coverage value was 45%, a confidence value was 100%, and an identity value was 69%. Validation of the model (MP) using the PROCHECK program showed the model was in the most favoured residue plot of 82.4%. This model deserves to be used as a model for calponin protein of snakehead fish, because the disallowed area was below 15%. The results of the analysis of interactions with other proteins using STRING-DB obtained the interaction model (MP) with Actin assembly-inducing protein (ACTA2) was 0.791; and Tropomyosin (TPM1) was 0.786. The results of molecular docking using PatchDock obtained the value of Atomic Contact Energy (ACE) for the calponin protein model (MP)-ACTA2 was 372.76 kJ/mol; Calponin model protein (MP)-TPM1 was 406.93 kJ/mol. The interactions that occured in the calponin model (MP)-ACTA2 were hydrogen bonds at residues Gly
Penelitian ini bertujuan untuk mengetahui efek steaming up selama kebuntingan tua terhadap profil protein darah induk kambing Peranakan Etawah. 12 ekor induk kambing dipilih berdasarkan periode laktasi kedua dan ketiga. Perlakuan pertama sebagai kontrol (P0), perlakuan kedua dan ketiga adalah steaming up menggunakan Gliricidia sepium 0,4% BK (P1) dan 0,8% BK (P2). Seluruh perlakuan diberikan pakan basal konsentrat 0,9% BK dan Pennisetum purpureum secara ad-libitum. Data dianalisis menggunakan Anova dengan Rancangan Acak Kelompok. Data profil protein darah induk kambing PE bunting tua dianalisis secara deskriptif eksploratif. Perlakuan Steaming up memberikan perbedaan yang nyata pada konsumsi BK, BO, dan PK (P<0,05). Praperlakuan steaming up menghasilkan 18 pita protein dengan berat molekul 15-158 kDa. Pasca perlakuan P0 menghasilkan 18 pita protein dengan berat molekul 15-158 kDa, P1 menghasilkan 19 pita protein dengan berat molekul 15-158 kDa. P2 menghasilkan 22 pita protein dengan berat molekul 15-158 kDa. Kesimpulan dari penelitian yaitu steaming up Gliricidia sepium sebesar 0,8% menghasilkan 22 pita protein dengan berat molekul yang berbeda. Banyaknya pita yang muncul dikaitkan dengan keberhasilan perlakuan steaming up pada kebuntingan tua.
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati, 2019
Penyusunan pustaka dari open reading frames (ORF) buatan yang tersusun atas 798 bp (pasangan basa), 576 di antaranya tersusun secara acak, yang mampu menyandi 266 asam amino telah berhasil dilakukan. Dalam upaya penyusunan tersebut diperoleh 32 transforman, lima di antaranya membawa ORF buatan. Dari kelima transforman yang membawa ORF buatan tersebut, hanya satu transforman yang mampu berekspresi dan menyandi suatu protein. Protein yang dihasilkan memiliki ukuran 17 kDa, berukuran lebih kecil daripada ukuran yang diharapkan yaitu 29 kDa.
Comparison of Computational Tools for Protein-Protein Interaction (PPI) Mapping and Analysis
Jurnal Teknologi, 2013
Several visualization tools for the mapping of protein-protein interactions have been developed in recent years. However, a systematic comparison of the virtues and limitations of different PPI visualization tools has not been carried out so far. In this study, we compare seven commonly used visualization tools, based on input and output file format, layout algorithm, database integration, Gene Ontology annotation and accessibility of each tool. The assessment was carried out based on brain disease datasets. Our suggested tools, NAViGaTOR, Cytoscape and Gephi perform competitively as PPI network visualization tools, can be a reference for future researches on PPI mapping and analysis.
Proteinlerin hücre içi yerleşimlerini bulmak için bir kümeleme yöntemi
2006
In this study, the focus is on predicting the subcellular localization of a protein, since subcellular localization is helpful in understanding a protein’s functions. Function of a protein may be estimated from its sequence. Motifs or conserved subsequences are strong indicators of function. In a given sample set of protein sequences known to perform the same function, a certain subsequence or group of subsequences should be common; that is, occurrence (frequency) of common subsequences should be high. Our idea is to find the common subsequences through clustering and use these common groups (implicit motifs) to classify proteins. To calculate the distance between two subsequences, traditional string edit distance is modified so that only replacement is allowed and the cost of replacement is related to an amino acid substitution matrix. Based on the modified string edit distance, spectral clustering embeds the subsequences into some transformed space for which the clustering problem...
Süt Proteinlerinin RP-HPLC ile Saptanması (İngilizce)
Gıda, 2015
Bu çalışmada, κ-, α- and β-kazein ile α-laktalbumin and β-laktoglobulin, bir RP kolonunun kullanıldığı HPLC-UV ile basit ve hızlı bir yöntem geliştirilerek saptanmıştır. Gradient elüsyonu, 1 ml/dk akış hızında ve 25 oC sıcaklıkta iki çözücü karışımı kullanılarak yürütülmüştür. A çözücüsü asetonitril: su:trifloroasetik asit (100:900:1) ve B çözücüsü asetonitril: su: trifloroasetik asit (100:900:1) karışımlarından oluşmaktadır. Akış, bir UV dedektörü kullanılarak 220 nm'de kaydedilmiştir. Farklı yöntemler kullanılarak RP-HPLC analizi için hazırlanan örneklerde, süt proteinlerine ait farklı kromatografik profiller elde edilmiştir. Diğer örnek hazırlama yöntemlerine kıyasla, enjeksiyondan önce belirtilen oranlarda A ve B çözücülerinin kullanıldığı örnek hazırlama yöntemi ile separasyonun daha keskin ve efektif olduğu ortaya konulmuştur. Bu çalışmada ortaya konulan örnek hazırlama tekniği ve elusyon pratiği ile, süt proteinlerinin analizi basit, hızlı ve duyarlı bir şekilde gerçekleş...