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Knowledge-based protein secondary structure assignment
- Proteins
, 1995
"... ABSTRACT We have developed an auto-matic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone tor-sional angle information. Parameters of the pattern recognition procedure were optimiz ..."
Abstract
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Cited by 324 (2 self)
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optimized using designations provided by the crystallog-raphers as a standard-of-truth. Comparison to the currently most widely used technique DSSP by Kabsch and Sander (Biopolymers 222577-2637, 1983) shows that STRIDE and DSSP as-sign secondary structural states in 58 and 31% of 226 protein chains in our
To Improve the Performance of Secondary Structure Prediction by Soft Computing Technique
"... Abstract — Proteins, one of the basic building blocks of all the organisms, need exploratory techniques to predict its complex structures. Machine learning technique such as neural network has been widely used in predicting secondary structures of amino acid sequences. Today, the main aim is to impr ..."
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. Binary bit encoding scheme is used to encode input training sequence in 3 state DSSP codes. The current efficiency achieved through this technique has reached up to 70 %.The experimental results reveal that the following proposed algorithm yields an improved performance with an accuracy of 80%.
BhairPred: prediction of b-hairpins in a protein from multiple alignment information using ANN and SVM techniques
, 2004
"... This paper describes a method for predicting a super-secondary structural motif, b-hairpins, in a protein sequence. The method was trained and tested on a set of 5102 hairpins and 5131 non-hairpins, obtained from a non-redundant dataset of 2880 proteins using the DSSP and PROMOTIF programs. Two mach ..."
Abstract
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Cited by 1 (0 self)
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This paper describes a method for predicting a super-secondary structural motif, b-hairpins, in a protein sequence. The method was trained and tested on a set of 5102 hairpins and 5131 non-hairpins, obtained from a non-redundant dataset of 2880 proteins using the DSSP and PROMOTIF programs. Two
A Bilinear Relaxation Based Algorithm for Concave Piecewise Linear Network Flow Problem
- Journal of Industrial and Management Optimization
"... We present a continuous relaxation technique for the Concave Piecewise Linear Network Flow Problem (CPLNFP), which has a bilinear objective function and network constraints. We show that a global optimum of the resulting problem is a solution of CPLNFP. The theo-retical results are generalized for a ..."
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Cited by 2 (2 self)
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We present a continuous relaxation technique for the Concave Piecewise Linear Network Flow Problem (CPLNFP), which has a bilinear objective function and network constraints. We show that a global optimum of the resulting problem is a solution of CPLNFP. The theo-retical results are generalized
Alexey Burtsev. Interrupt mechanism for threaded code interpreter. 1 Interrupt mechanism for threaded code interpreter
"... Various methods to support interrupt mechanism in programming systems, based on threaded code techniques, are analysed. Threaded code interpreters, which support interrupt handling at the level of machine code, have serious demerits. Another method of interruption for interpreter of threaded code ar ..."
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procedure, which body are defined in machine code). Realization of interrupt mechanism according to this suggested method for DSSP (Forth-like system, developed in Moscow University) are described. Advantages of new interrupt technique for threaded code interpreter, especially concerning parallel
Artificial Neural Network aided Protein Structure Prediction
"... Protein structure prediction plays a vital role in drug design and biotechnology. Understanding protein structures is necessary to determine the function of a protein and its interaction with DNA, RNA and Enzymes. Experimental techniques such as NMR Spectroscopy and X-ray Crystallography have been t ..."
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Protein structure prediction plays a vital role in drug design and biotechnology. Understanding protein structures is necessary to determine the function of a protein and its interaction with DNA, RNA and Enzymes. Experimental techniques such as NMR Spectroscopy and X-ray Crystallography have been
RESEARCH ARTICLE Quantitative Analysis of Torso FDG-PET Scans by Using Anatomical Standardization of Normal Cases from Thorough Physical Examinations
"... Understanding of standardized uptake value (SUV) of 2-deoxy-2-[18F]fluoro-d-glucose pos-itron emission tomography (FDG-PET) depends on the background accumulations of glu-cose because the SUV often varies the status of patients. The purpose of this study was to develop a new method for quantitative ..."
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analysis of SUV of FDG-PET scan images. The method included an anatomical standardization and a statistical comparison with normal cases by using Z-score that are often used in SPM or 3D-SSP approach for brain function analysis. Our scheme consisted of two approaches, which included the construction of a
