Assigning protein functions using PSI-BLAST
Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST
... by using a scoring scheme that includes a 20 × 20 amino acid substitution matrix and a penalty function for ...by using a pairwise comparison score ...
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Prediction of α-turns in proteins using PSI-BLAST profiles and secondary structure information
... Proteins Using PSI-BLAST Profiles and Secondary Structure Information Harpreet Kaur and ...of protein struc- ture prediction have been tried in this study, which includes statistical approach ...
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LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST
... a protein is one of the key functional characters as proteins must be localized correctly at the subcellular level to have normal biological ...of protein subcellular location is very desirable, especially ...
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Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
... known protein structures determined which exhibit conforma- tional heterogeneity of one or more prolyl peptide bonds ...in protein structure and ...in protein folding has been well characterized ...
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BLAST-based structural annotation of protein residues using Protein Data Bank
... simple BLAST based server for annotation of ...Despite BLAST have been developed two decades back and has been citeed by ~54,000 research artilces, it is difficult for a biologist to annotate a query ...
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ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST
... addition, PSI-BLAST was also used to search the query sequence against the dataset of proteins (experimentally annotated proteins) to predict its subcellular ...module using all features of a ...
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Evaluation of function predictions by PFP, ESG, and PSI BLAST for moonlighting proteins
... moonlighting functions of a protein is important for automatic function ...and PSI- BLAST in predicting the functional diversity of moon- lighting ...moonlighting functions as com- ...
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PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations
... cellular functions such as gene regulation, metabolism and cell ...new protein sequence, it is fundamental to understand its 3D ...of protein structural class provides useful information towards the ...
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Using indirect protein interactions for the prediction of Gene Ontology functions
... Effectiveness of FS-Weight The effectiveness of FS-Weighted Averaging for function prediction depends upon the capability of FS-Weight in assigning higher weights to direct and indirect interac- tions that involve ...
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List of proteins that were listed as both a beta lactamase and a 6-aminohexanoate hydrolase nylonase in GenBank that were determined by searching for NylB homologs using psi-BLAST
... binding protein transpeptidase domain; for GenBank A0A011QU85 alignment was was detected with superfamily member COG1680 pfam00144 = Beta-lactamase; This family appears to be distantly related to pfam00905 and ...
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Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix
... represent protein sequences on PSSM, which can characterize the subsequence of amino acids in the conserved regions and capture the useful evolutionary information; (2) PCA (Principal Component Analysis) method ...
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Some properties of functions related to the gamma, psi and tetragamma functions
... a b s t r a c t In this paper, some properties associated with the complete monotonicity and the logarithmically complete monotonicity of functions related to the gamma, psi and tetragamma functions ...
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Three Classes of Logarithmically Completely Monotonic Functions Involving Gamma and Psi Functions
... MONOTONIC FUNCTIONS INVOLVING GAMMA AND PSI FUNCTIONS FENG QI ...of functions involving Euler’s gamma function and originating from certain problems of traffic flow are proved to be ...
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Assigning roles to protein mentions: The case of transcription factors
... Conditional Random Fields (CRFs) are discriminatively undi- rected graphic models, a special case of which is a linear chain that corresponds to a condition trained finite-state machine [23]. Un- like other graphical ...
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Importance of functional programming Assigning functions to variables, arrays, and other data structures Passing functions to other functions Returning functions from functions Making anonymous functions Capturing local variables (making closures) Using the apply and call methods
... • Using the apply and call methods For additional materials, please see http://www.coreservlets.com/. The JavaScript tutorial section contains complete source code for all examples in the entire tutorial series, ...
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Necessary and sufficient conditions for functions involving the psi function to be completely monotonic
... 28. Mortici, C: New bounds for a convergence by DeTemple. J. Sci. Arts 13(2), 239-242 (2010) 29. Batir, N: Inequalities for the gamma function. Arch. Math. 91(6), 554-563 (2008) 30. Qi, F, Guo, B-N: Sharp inequalities ...
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A Double Inequality for Divided Differences and Some Identities of Psi and Polygamma Functions
... A DOUBLE INEQUALITY FOR DIVIDED DIFFERENCES AND SOME IDENTITIES OF PSI AND POLYGAMMA FUNCTIONS FENG QI Abstract. In this short note, from the logarithmically completely monotonic property of the function (x ...
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Identification of giant Mimivirus protein functions using RNA interference
... known functions (ORFans). We knocked down Mimivirus genes using short interfering RNA as a proof of concept to determine the functions of giant virus ...a protein absent in a Mimivirus mutant ...
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Protein secondary structure prediction using BLAST and relaxed threshold rule induction from coverings
... The application of artificial neural network methods to this problem is revolutionary in the sense that those techniques employ the homologues of proteins for training and prediction. In this dissertation, a different ...
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A Completely Monotonic Function Involving Divided Differences of Psi and Polygamma Functions and an Application
... Abstract. A function involving the divided differences of the psi function and the polygamma functions is proved to be completely monotonic. As an appli- cation of this result, the monotonicity and ...
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