PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines

Secondary structure prediction is a crucial task for understanding the variety of protein structures and performed biological functions. Prediction of secondary structures for new proteins using their amino acid sequences is of fundamental importance in bioinformatics. We propose a novel technique to predict protein secondary structures based on position-specific scoring matrices (PSSMs) and physico-chemical properties of amino acids. It is a two stage approach involving multiclass support vector machines (SVMs) as classifiers for three different structural conformations, viz., helix, sheet and coil. In the first stage, PSSMs obtained from PSI-BLAST and five specially selected physicochemical properties of amino acids are fed into SVMs as features for sequence-to-structure prediction. Confidence values for forming helix, sheet and coil that are obtained from the first stage SVM are then used in the second stage SVM for performing structure-to-structure prediction. The two-stage cascaded classifiers (PSP_MCSVM) are trained with proteins from RS126 dataset. The classifiers are finally tested on target proteins of critical assessment of protein structure prediction experiment-9 (CASP9). PSP_MCSVM with brainstorming consensus procedure performs better than the prediction servers like Predator, DSC, SIMPA96, for randomly selected proteins from CASP9 targets. The overall performance is found to be comparable with the current state-of-the art. PSP_MCSVM source code, train-test datasets and supplementary files are available freely in public domain at: http://sysbio.icm.edu.pl/secstruct and http://code.google.com/p/cmater-bioinfo

Stereochemistry of organic compounds : Principles and applications

xxiii, 564 p. ; 24 cm

Synthetic studies in the diterpene series. Part VIII. Synthesis of miltirone, a diterpenoid quinone

Miltirone (I), a diterpenoid quinone has been synthesised from p-bromoanisole, the key intermediate being 6-isopropyl-7-methoxy-1-tetralone (VI). A Reformatsky reaction on compound (VI) with methyl γ -bromocrotonate, followed by aromatisation, treatment with methylmagnesium iodide, and cyclisation gave 1,2,3,4-tetrahydro-1,1 -dimethyl-6-methoxy-7-isopropylphenanthrene. The corresponding phenol was oxidised to a quinone, identical with miltirone, either by air or by Fremy's salt

COMPARATIVE STUDY OF DISTANCE METRICS FOR FINDING SKIN COLOR SIMILARITY OF TWO COLOR FACIAL IMAGES

This paper describes the comparative study of performance between the existing distance metrics like Manhattan, Euclidean, Vector Cosine Angle and Modified Euclidean distance for finding the similarity of complexion by calculating the distance between the skin colors of two color facial images. The existing methodologies have been tested on 110 male and 40 female facial images taken from FRAV2D database. To verify the result obtained from the existing methodologies an opinion poll of 100 peoples have been taken. The experimental result shows that the result obtained by the methodologies of Manhattan, Euclidean and Vector Cosine Angle distance contradict the survey result in 80 % cases and for Modified Euclidean distance methodology the contradiction arises in 60 % cases. The present work has been implemented using Matlab 7